Starting phenix.real_space_refine on Tue Jan 21 10:54:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9y_39872/01_2025/8z9y_39872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9y_39872/01_2025/8z9y_39872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9y_39872/01_2025/8z9y_39872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9y_39872/01_2025/8z9y_39872.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9y_39872/01_2025/8z9y_39872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9y_39872/01_2025/8z9y_39872.cif" } resolution = 2.5 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= 0.100 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: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 10913 2.51 5 N 2771 2.21 5 O 2908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16671 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6636 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 751} Chain breaks: 14 Chain: "B" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1386 Classifications: {'peptide': 164} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 151} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 811 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain: "D" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3782 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 416} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 361} Chain: "F" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 801 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Time building chain proxies: 9.63, per 1000 atoms: 0.58 Number of scatterers: 16671 At special positions: 0 Unit cell: (108.7, 113.048, 156.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 2908 8.00 N 2771 7.00 C 10913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 349 " - pdb=" SG CYS D 375 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 2.1 seconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3754 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 7 sheets defined 56.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.733A pdb=" N LEU A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.595A pdb=" N ARG A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 78 removed outlier: 4.218A pdb=" N GLU A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 90 through 110 removed outlier: 4.528A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.698A pdb=" N GLN A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 151 through 164 removed outlier: 3.843A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 196 removed outlier: 3.846A pdb=" N ILE A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 241 removed outlier: 3.774A pdb=" N ALA A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 414 removed outlier: 3.577A pdb=" N SER A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 456 removed outlier: 3.697A pdb=" N LEU A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.541A pdb=" N ILE A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 615 through 618 removed outlier: 3.944A pdb=" N LEU A 618 " --> pdb=" O LEU A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 707 through 712 removed outlier: 4.278A pdb=" N ASP A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1141 Processing helix chain 'A' and resid 1152 through 1162 Processing helix chain 'A' and resid 1169 through 1179 removed outlier: 3.792A pdb=" N ILE A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1198 Processing helix chain 'A' and resid 1215 through 1221 removed outlier: 3.507A pdb=" N ASN A1219 " --> pdb=" O ASN A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1248 removed outlier: 4.712A pdb=" N VAL A1238 " --> pdb=" O TRP A1234 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A1248 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1304 removed outlier: 3.628A pdb=" N ASP A1292 " --> pdb=" O ASN A1288 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1293 " --> pdb=" O VAL A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1422 No H-bonds generated for 'chain 'A' and resid 1420 through 1422' Processing helix chain 'A' and resid 1423 through 1433 Processing helix chain 'A' and resid 1438 through 1443 Processing helix chain 'A' and resid 1534 through 1541 Processing helix chain 'A' and resid 1542 through 1544 No H-bonds generated for 'chain 'A' and resid 1542 through 1544' Processing helix chain 'A' and resid 1622 through 1637 removed outlier: 4.170A pdb=" N ILE A1633 " --> pdb=" O ARG A1629 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER A1634 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A1635 " --> pdb=" O ILE A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1685 Processing helix chain 'A' and resid 1687 through 1701 removed outlier: 3.953A pdb=" N ARG A1692 " --> pdb=" O PRO A1688 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A1693 " --> pdb=" O LYS A1689 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A1701 " --> pdb=" O LEU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1736 through 1745 Processing helix chain 'A' and resid 1749 through 1763 removed outlier: 4.464A pdb=" N LEU A1753 " --> pdb=" O PRO A1749 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU A1754 " --> pdb=" O ASN A1750 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1777 Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.603A pdb=" N ARG B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 143 through 150 removed outlier: 3.932A pdb=" N HIS B 148 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS B 150 " --> pdb=" O TYR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.713A pdb=" N ASP B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.890A pdb=" N LEU B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE B 180 " --> pdb=" O MET B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.621A pdb=" N HIS B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 4.254A pdb=" N ALA B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 229 through 254 removed outlier: 3.667A pdb=" N ALA B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 270 Processing helix chain 'C' and resid 20 through 40 removed outlier: 3.517A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.654A pdb=" N LEU C 46 " --> pdb=" O MET C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 71 removed outlier: 4.015A pdb=" N LYS C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 82 through 97 removed outlier: 3.802A pdb=" N ARG C 86 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Proline residue: C 94 - end of helix Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.504A pdb=" N VAL D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 271 through 280 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.872A pdb=" N MET D 289 " --> pdb=" O ARG D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 Processing helix chain 'D' and resid 315 through 318 Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.171A pdb=" N VAL D 323 " --> pdb=" O ASN D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 395 Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 431 through 437 removed outlier: 3.686A pdb=" N ASN D 434 " --> pdb=" O GLY D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 443 through 463 removed outlier: 3.851A pdb=" N PHE D 461 " --> pdb=" O TRP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 467 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'E' and resid 65 through 81 removed outlier: 3.780A pdb=" N ILE E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 95 Processing helix chain 'E' and resid 106 through 122 removed outlier: 3.639A pdb=" N GLU E 110 " --> pdb=" O PRO E 106 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 147 Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 156 through 163 removed outlier: 3.770A pdb=" N ILE E 163 " --> pdb=" O TYR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 201 Processing helix chain 'E' and resid 215 through 221 removed outlier: 3.938A pdb=" N ALA E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 235 removed outlier: 3.725A pdb=" N LYS E 235 " --> pdb=" O ASP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 Processing helix chain 'E' and resid 288 through 294 removed outlier: 3.725A pdb=" N ALA E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 314 Processing helix chain 'E' and resid 328 through 350 removed outlier: 3.504A pdb=" N ASN E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 365 removed outlier: 3.538A pdb=" N PHE E 365 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 372 through 378 Processing helix chain 'E' and resid 388 through 399 Processing helix chain 'E' and resid 403 through 418 removed outlier: 3.890A pdb=" N VAL E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 455 removed outlier: 4.089A pdb=" N ARG E 439 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 440 " --> pdb=" O PRO E 436 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 179 removed outlier: 4.014A pdb=" N LEU F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 removed outlier: 4.810A pdb=" N LYS F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 226 removed outlier: 4.061A pdb=" N LEU F 206 " --> pdb=" O LYS F 202 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG F 208 " --> pdb=" O VAL F 204 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TRP F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 Processing helix chain 'F' and resid 244 through 251 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 390 Processing sheet with id=AA2, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AA3, first strand: chain 'A' and resid 612 through 613 removed outlier: 6.751A pdb=" N ILE A 612 " --> pdb=" O ILE A 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1546 through 1550 removed outlier: 4.065A pdb=" N ARG A1546 " --> pdb=" O VAL A1615 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 207 through 212 removed outlier: 6.581A pdb=" N SER D 218 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 233 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU D 220 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LYS D 231 " --> pdb=" O GLU D 220 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR D 222 " --> pdb=" O GLN D 229 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N HIS D 255 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN D 340 " --> pdb=" O CYS D 349 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N CYS D 349 " --> pdb=" O GLN D 340 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS D 342 " --> pdb=" O HIS D 347 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N HIS D 347 " --> pdb=" O LYS D 342 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 361 " --> pdb=" O GLY D 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 487 through 490 removed outlier: 4.829A pdb=" N ILE D 520 " --> pdb=" O GLN D 536 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 248 through 252 removed outlier: 5.829A pdb=" N TRP E 239 " --> pdb=" O PRO E 251 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE E 271 " --> pdb=" O LYS E 242 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4875 1.34 - 1.46: 3368 1.46 - 1.58: 8812 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 17193 Sorted by residual: bond pdb=" C PRO D 537 " pdb=" N PRO D 538 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.22e-02 6.72e+03 4.86e+00 bond pdb=" N GLU F 185 " pdb=" CA GLU F 185 " ideal model delta sigma weight residual 1.456 1.481 -0.024 1.31e-02 5.83e+03 3.47e+00 bond pdb=" CB GLU F 184 " pdb=" CG GLU F 184 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" C THR F 182 " pdb=" O THR F 182 " ideal model delta sigma weight residual 1.236 1.221 0.016 1.18e-02 7.18e+03 1.78e+00 bond pdb=" CB PHE E 452 " pdb=" CG PHE E 452 " ideal model delta sigma weight residual 1.502 1.532 -0.030 2.30e-02 1.89e+03 1.74e+00 ... (remaining 17188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 23126 3.21 - 6.42: 135 6.42 - 9.64: 19 9.64 - 12.85: 3 12.85 - 16.06: 2 Bond angle restraints: 23285 Sorted by residual: angle pdb=" CA LYS C 71 " pdb=" CB LYS C 71 " pdb=" CG LYS C 71 " ideal model delta sigma weight residual 114.10 127.38 -13.28 2.00e+00 2.50e-01 4.41e+01 angle pdb=" N PRO D 170 " pdb=" CA PRO D 170 " pdb=" CB PRO D 170 " ideal model delta sigma weight residual 102.88 110.10 -7.22 1.09e+00 8.42e-01 4.39e+01 angle pdb=" C GLU A 374 " pdb=" CA GLU A 374 " pdb=" CB GLU A 374 " ideal model delta sigma weight residual 115.79 108.81 6.98 1.19e+00 7.06e-01 3.44e+01 angle pdb=" CA LYS F 219 " pdb=" CB LYS F 219 " pdb=" CG LYS F 219 " ideal model delta sigma weight residual 114.10 123.77 -9.67 2.00e+00 2.50e-01 2.34e+01 angle pdb=" CA LEU F 186 " pdb=" CB LEU F 186 " pdb=" CG LEU F 186 " ideal model delta sigma weight residual 116.30 132.36 -16.06 3.50e+00 8.16e-02 2.11e+01 ... (remaining 23280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 8460 16.50 - 33.01: 1222 33.01 - 49.51: 343 49.51 - 66.01: 75 66.01 - 82.52: 24 Dihedral angle restraints: 10124 sinusoidal: 4304 harmonic: 5820 Sorted by residual: dihedral pdb=" CA PHE D 115 " pdb=" C PHE D 115 " pdb=" N PRO D 116 " pdb=" CA PRO D 116 " ideal model delta harmonic sigma weight residual 180.00 149.35 30.65 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA LYS A 372 " pdb=" C LYS A 372 " pdb=" N ILE A 373 " pdb=" CA ILE A 373 " ideal model delta harmonic sigma weight residual -180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA TRP A 108 " pdb=" C TRP A 108 " pdb=" N ASN A 109 " pdb=" CA ASN A 109 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 10121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1856 0.050 - 0.101: 424 0.101 - 0.151: 81 0.151 - 0.201: 5 0.201 - 0.252: 2 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA PRO D 170 " pdb=" N PRO D 170 " pdb=" C PRO D 170 " pdb=" CB PRO D 170 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE F 180 " pdb=" N ILE F 180 " pdb=" C ILE F 180 " pdb=" CB ILE F 180 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU F 184 " pdb=" N GLU F 184 " pdb=" C GLU F 184 " pdb=" CB GLU F 184 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 2365 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 187 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C VAL F 187 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL F 187 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS F 188 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 115 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO D 116 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 470 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO D 471 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 471 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 471 " -0.031 5.00e-02 4.00e+02 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 428 2.71 - 3.26: 16233 3.26 - 3.80: 26663 3.80 - 4.35: 34007 4.35 - 4.90: 56944 Nonbonded interactions: 134275 Sorted by model distance: nonbonded pdb=" CZ ARG A1761 " pdb=" CZ PHE D 461 " model vdw 2.160 2.856 nonbonded pdb=" O ILE F 180 " pdb=" N GLY F 183 " model vdw 2.169 3.120 nonbonded pdb=" O ILE F 174 " pdb=" OG1 THR F 178 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR A1544 " pdb=" O LEU D 136 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG A1761 " pdb=" CD1 PHE D 461 " model vdw 2.214 3.420 ... (remaining 134270 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.680 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.003 0.051 17193 Z= 0.177 Angle : 0.651 16.059 23285 Z= 0.337 Chirality : 0.043 0.252 2368 Planarity : 0.005 0.062 2952 Dihedral : 16.902 82.516 6367 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.86 % Favored : 93.04 % Rotamer: Outliers : 0.11 % Allowed : 23.25 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.55 (0.20), residues: 1940 helix: 1.50 (0.17), residues: 987 sheet: 0.90 (0.62), residues: 82 loop : -1.05 (0.23), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 123 HIS 0.004 0.001 HIS C 63 PHE 0.033 0.001 PHE F 173 TYR 0.015 0.001 TYR F 226 ARG 0.009 0.000 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 2.007 Fit side-chains REVERT: A 17 MET cc_start: 0.6574 (tpt) cc_final: 0.6220 (tpt) REVERT: A 20 ILE cc_start: 0.7687 (mm) cc_final: 0.7391 (tp) REVERT: A 75 MET cc_start: 0.8279 (tpt) cc_final: 0.7956 (mmm) REVERT: A 125 MET cc_start: 0.5374 (mpp) cc_final: 0.3958 (mtt) REVERT: A 129 ARG cc_start: 0.5358 (tpt90) cc_final: 0.5013 (tpt90) REVERT: A 186 MET cc_start: 0.5094 (mtm) cc_final: 0.4591 (mtt) REVERT: A 410 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7519 (mp0) REVERT: A 595 MET cc_start: -0.0144 (ppp) cc_final: -0.0947 (mmt) REVERT: A 668 MET cc_start: 0.3953 (pmm) cc_final: 0.3291 (ptm) REVERT: A 701 PHE cc_start: 0.7044 (m-10) cc_final: 0.6794 (m-80) REVERT: A 1144 MET cc_start: 0.4558 (tpp) cc_final: 0.3629 (ttt) REVERT: A 1185 PHE cc_start: 0.5785 (t80) cc_final: 0.5472 (t80) REVERT: A 1193 PHE cc_start: 0.7318 (t80) cc_final: 0.6992 (t80) REVERT: A 1225 TYR cc_start: 0.8192 (t80) cc_final: 0.7852 (t80) REVERT: A 1605 MET cc_start: 0.4080 (tmm) cc_final: 0.3507 (mmm) REVERT: A 1737 LYS cc_start: 0.6395 (tttp) cc_final: 0.5558 (pmtt) REVERT: B 116 MET cc_start: 0.1987 (tpp) cc_final: 0.1037 (mtp) REVERT: B 179 PHE cc_start: 0.3058 (t80) cc_final: 0.2334 (m-80) REVERT: B 204 MET cc_start: 0.5317 (ppp) cc_final: 0.4653 (tmm) REVERT: B 229 PHE cc_start: 0.7173 (t80) cc_final: 0.6902 (t80) REVERT: C 17 HIS cc_start: 0.6184 (m-70) cc_final: 0.5968 (m170) REVERT: C 88 SER cc_start: 0.7921 (m) cc_final: 0.7546 (t) REVERT: D 288 TYR cc_start: 0.8518 (m-80) cc_final: 0.8095 (m-80) REVERT: D 353 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 452 GLN cc_start: 0.8182 (tt0) cc_final: 0.7758 (mt0) REVERT: D 455 GLU cc_start: 0.8427 (tp30) cc_final: 0.7663 (tp30) REVERT: D 528 LYS cc_start: 0.7146 (mtmm) cc_final: 0.6745 (ttmm) REVERT: E 73 GLN cc_start: 0.6552 (tp-100) cc_final: 0.5881 (tp40) REVERT: E 119 GLU cc_start: 0.6317 (mm-30) cc_final: 0.6110 (mm-30) REVERT: E 122 ARG cc_start: 0.6821 (mtm110) cc_final: 0.6132 (mtm180) REVERT: E 142 LYS cc_start: 0.7754 (ttpp) cc_final: 0.7453 (ttpt) REVERT: E 227 LYS cc_start: 0.7972 (ttpp) cc_final: 0.7603 (ttpp) REVERT: E 350 ASN cc_start: 0.8536 (t0) cc_final: 0.8273 (t0) REVERT: E 380 ASP cc_start: 0.7700 (t0) cc_final: 0.7341 (t0) REVERT: E 443 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6772 (mtm110) REVERT: F 247 LYS cc_start: 0.5560 (mttp) cc_final: 0.4719 (ttpp) outliers start: 2 outliers final: 1 residues processed: 240 average time/residue: 1.4838 time to fit residues: 392.5654 Evaluate side-chains 212 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN C 51 ASN D 476 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.192656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141248 restraints weight = 20561.891| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.07 r_work: 0.3787 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17193 Z= 0.214 Angle : 0.624 11.529 23285 Z= 0.323 Chirality : 0.044 0.178 2368 Planarity : 0.006 0.142 2952 Dihedral : 4.759 29.927 2187 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.20 % Rotamer: Outliers : 2.80 % Allowed : 21.96 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.51 (0.20), residues: 1940 helix: 1.47 (0.17), residues: 993 sheet: 0.97 (0.58), residues: 90 loop : -1.13 (0.23), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 160 HIS 0.005 0.001 HIS C 63 PHE 0.030 0.002 PHE F 173 TYR 0.017 0.002 TYR F 177 ARG 0.013 0.001 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.6864 (tpt) cc_final: 0.6636 (tpt) REVERT: A 20 ILE cc_start: 0.8141 (mm) cc_final: 0.7758 (tp) REVERT: A 75 MET cc_start: 0.8528 (tpt) cc_final: 0.8201 (mmm) REVERT: A 125 MET cc_start: 0.5325 (mpp) cc_final: 0.3899 (mtt) REVERT: A 129 ARG cc_start: 0.5792 (tpt90) cc_final: 0.5562 (tpt90) REVERT: A 186 MET cc_start: 0.5503 (mtm) cc_final: 0.4941 (mtt) REVERT: A 494 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7019 (mtm180) REVERT: A 668 MET cc_start: 0.4097 (pmm) cc_final: 0.3246 (ptm) REVERT: A 701 PHE cc_start: 0.7531 (m-10) cc_final: 0.7261 (m-80) REVERT: A 1185 PHE cc_start: 0.5947 (t80) cc_final: 0.5615 (t80) REVERT: A 1193 PHE cc_start: 0.7429 (t80) cc_final: 0.7204 (t80) REVERT: A 1225 TYR cc_start: 0.8203 (t80) cc_final: 0.7886 (t80) REVERT: A 1605 MET cc_start: 0.4193 (tmm) cc_final: 0.3594 (mmm) REVERT: A 1737 LYS cc_start: 0.6675 (tttp) cc_final: 0.5855 (pmtt) REVERT: B 116 MET cc_start: 0.1911 (tpp) cc_final: 0.0987 (mtp) REVERT: B 157 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6230 (tt0) REVERT: B 179 PHE cc_start: 0.3657 (t80) cc_final: 0.2825 (m-80) REVERT: B 204 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5306 (tmm) REVERT: D 125 GLN cc_start: 0.8105 (mp10) cc_final: 0.7821 (mp10) REVERT: D 165 ASP cc_start: 0.7950 (t70) cc_final: 0.7459 (t70) REVERT: D 259 ASP cc_start: 0.7686 (m-30) cc_final: 0.7363 (m-30) REVERT: D 282 ARG cc_start: 0.7007 (mtp180) cc_final: 0.6743 (mtp180) REVERT: D 288 TYR cc_start: 0.8835 (m-80) cc_final: 0.8423 (m-80) REVERT: D 388 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8047 (mm-30) REVERT: D 452 GLN cc_start: 0.8598 (tt0) cc_final: 0.8308 (mt0) REVERT: D 455 GLU cc_start: 0.8729 (tp30) cc_final: 0.8173 (tp30) REVERT: D 528 LYS cc_start: 0.7193 (mtmm) cc_final: 0.6805 (ttmm) REVERT: E 73 GLN cc_start: 0.7167 (tp-100) cc_final: 0.6543 (tp40) REVERT: E 119 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6512 (mm-30) REVERT: E 122 ARG cc_start: 0.7375 (mtm110) cc_final: 0.6696 (mtm180) REVERT: E 142 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7993 (ttpt) REVERT: E 144 GLU cc_start: 0.7745 (tp30) cc_final: 0.7366 (tt0) REVERT: E 227 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8071 (ttpp) REVERT: E 350 ASN cc_start: 0.8584 (t0) cc_final: 0.8357 (t0) REVERT: E 443 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7296 (mtm110) REVERT: F 247 LYS cc_start: 0.5373 (mttp) cc_final: 0.4776 (ttpp) outliers start: 50 outliers final: 20 residues processed: 248 average time/residue: 1.4796 time to fit residues: 406.8440 Evaluate side-chains 226 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1197 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1447 ASN C 17 HIS C 51 ASN E 69 GLN E 331 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.188222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134522 restraints weight = 20582.965| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.08 r_work: 0.3728 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 17193 Z= 0.346 Angle : 0.692 9.956 23285 Z= 0.360 Chirality : 0.048 0.200 2368 Planarity : 0.008 0.244 2952 Dihedral : 5.243 33.330 2187 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.53 % Favored : 92.42 % Rotamer: Outliers : 4.54 % Allowed : 20.56 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.00 (0.20), residues: 1940 helix: 1.04 (0.17), residues: 990 sheet: 0.99 (0.56), residues: 89 loop : -1.37 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 160 HIS 0.007 0.002 HIS A 105 PHE 0.028 0.002 PHE F 173 TYR 0.027 0.002 TYR F 226 ARG 0.011 0.001 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 218 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8216 (mm) cc_final: 0.7740 (tp) REVERT: A 75 MET cc_start: 0.8552 (tpt) cc_final: 0.8160 (mmm) REVERT: A 125 MET cc_start: 0.5388 (mpp) cc_final: 0.4041 (mtt) REVERT: A 186 MET cc_start: 0.5700 (mtm) cc_final: 0.5040 (mtt) REVERT: A 410 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: A 494 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.4940 (mtp180) REVERT: A 668 MET cc_start: 0.4323 (OUTLIER) cc_final: 0.3301 (ptm) REVERT: A 672 ARG cc_start: 0.4456 (OUTLIER) cc_final: 0.2906 (tpp80) REVERT: A 701 PHE cc_start: 0.7529 (m-10) cc_final: 0.7234 (m-80) REVERT: A 1144 MET cc_start: 0.3979 (tpp) cc_final: 0.3225 (ttm) REVERT: A 1185 PHE cc_start: 0.6376 (t80) cc_final: 0.5923 (t80) REVERT: A 1193 PHE cc_start: 0.7546 (t80) cc_final: 0.7324 (t80) REVERT: A 1225 TYR cc_start: 0.8154 (t80) cc_final: 0.7819 (t80) REVERT: A 1605 MET cc_start: 0.4536 (tmm) cc_final: 0.3744 (mmm) REVERT: A 1737 LYS cc_start: 0.6728 (tttp) cc_final: 0.5885 (pmtt) REVERT: B 116 MET cc_start: 0.2145 (tpp) cc_final: 0.1361 (mtm) REVERT: B 157 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6211 (tt0) REVERT: B 158 PHE cc_start: 0.6427 (m-80) cc_final: 0.6206 (m-10) REVERT: B 179 PHE cc_start: 0.3805 (t80) cc_final: 0.2982 (m-80) REVERT: B 195 PHE cc_start: 0.4730 (t80) cc_final: 0.4489 (t80) REVERT: B 204 MET cc_start: 0.5826 (OUTLIER) cc_final: 0.5513 (tmm) REVERT: B 218 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6305 (mtmp) REVERT: C 97 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: D 125 GLN cc_start: 0.8173 (mp10) cc_final: 0.7971 (mp10) REVERT: D 282 ARG cc_start: 0.6998 (mtp180) cc_final: 0.6658 (mtp180) REVERT: D 288 TYR cc_start: 0.8835 (m-80) cc_final: 0.8346 (m-80) REVERT: D 452 GLN cc_start: 0.8609 (tt0) cc_final: 0.8386 (mt0) REVERT: D 455 GLU cc_start: 0.8818 (tp30) cc_final: 0.8275 (tp30) REVERT: D 520 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6193 (tp) REVERT: D 533 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7694 (pp) REVERT: E 73 GLN cc_start: 0.7289 (tp-100) cc_final: 0.6548 (tp-100) REVERT: E 142 LYS cc_start: 0.8381 (ttpp) cc_final: 0.8081 (ttpt) REVERT: E 144 GLU cc_start: 0.7851 (tp30) cc_final: 0.7611 (tt0) REVERT: E 227 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8175 (ttpp) REVERT: E 443 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7216 (mtm110) REVERT: F 247 LYS cc_start: 0.5851 (mttp) cc_final: 0.5226 (ttpp) outliers start: 81 outliers final: 39 residues processed: 272 average time/residue: 1.4063 time to fit residues: 423.7712 Evaluate side-chains 253 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 480 TYR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 160 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 176 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1219 ASN ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1447 ASN B 194 HIS B 211 GLN C 17 HIS C 51 ASN E 69 GLN E 416 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.190641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136641 restraints weight = 20537.286| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.13 r_work: 0.3776 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17193 Z= 0.188 Angle : 0.602 11.385 23285 Z= 0.312 Chirality : 0.044 0.208 2368 Planarity : 0.006 0.155 2952 Dihedral : 4.937 32.571 2187 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 3.70 % Allowed : 22.13 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.19 (0.20), residues: 1940 helix: 1.23 (0.17), residues: 996 sheet: 1.06 (0.55), residues: 89 loop : -1.34 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 123 HIS 0.004 0.001 HIS C 63 PHE 0.029 0.001 PHE F 173 TYR 0.023 0.001 TYR F 226 ARG 0.017 0.000 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8203 (mm) cc_final: 0.7715 (tp) REVERT: A 75 MET cc_start: 0.8581 (tpt) cc_final: 0.8169 (mmm) REVERT: A 125 MET cc_start: 0.5420 (mpp) cc_final: 0.4049 (mtt) REVERT: A 185 PHE cc_start: 0.5842 (OUTLIER) cc_final: 0.5070 (p90) REVERT: A 186 MET cc_start: 0.5567 (mtm) cc_final: 0.4890 (mtt) REVERT: A 238 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6249 (t80) REVERT: A 494 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6981 (mtm180) REVERT: A 668 MET cc_start: 0.4267 (OUTLIER) cc_final: 0.3272 (ptm) REVERT: A 672 ARG cc_start: 0.4450 (OUTLIER) cc_final: 0.2877 (tpp80) REVERT: A 701 PHE cc_start: 0.7493 (m-10) cc_final: 0.7214 (m-80) REVERT: A 1185 PHE cc_start: 0.6220 (t80) cc_final: 0.5752 (t80) REVERT: A 1193 PHE cc_start: 0.7608 (t80) cc_final: 0.7305 (t80) REVERT: A 1225 TYR cc_start: 0.8121 (t80) cc_final: 0.7825 (t80) REVERT: A 1605 MET cc_start: 0.4200 (tmm) cc_final: 0.3391 (mmm) REVERT: A 1737 LYS cc_start: 0.6715 (tttp) cc_final: 0.5893 (pmtt) REVERT: B 116 MET cc_start: 0.1986 (tpp) cc_final: 0.1332 (mtm) REVERT: B 157 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6099 (tt0) REVERT: B 158 PHE cc_start: 0.6229 (m-80) cc_final: 0.5996 (m-10) REVERT: B 179 PHE cc_start: 0.3880 (t80) cc_final: 0.2996 (m-80) REVERT: B 204 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.5393 (tmm) REVERT: B 218 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.6252 (mtmp) REVERT: B 271 ILE cc_start: 0.5264 (OUTLIER) cc_final: 0.4821 (tt) REVERT: C 97 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: D 282 ARG cc_start: 0.6958 (mtp180) cc_final: 0.6691 (mtp180) REVERT: D 452 GLN cc_start: 0.8527 (tt0) cc_final: 0.8322 (mt0) REVERT: D 455 GLU cc_start: 0.8823 (tp30) cc_final: 0.8276 (tp30) REVERT: D 528 LYS cc_start: 0.7091 (mtmm) cc_final: 0.6686 (ttmm) REVERT: E 73 GLN cc_start: 0.7240 (tp-100) cc_final: 0.6680 (tp40) REVERT: E 142 LYS cc_start: 0.8301 (ttpp) cc_final: 0.8008 (ttpt) REVERT: E 227 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8109 (ttpp) REVERT: E 350 ASN cc_start: 0.8654 (t0) cc_final: 0.8390 (t0) REVERT: E 419 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6312 (m-80) REVERT: E 443 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7322 (mtm110) REVERT: F 181 ILE cc_start: 0.0914 (OUTLIER) cc_final: 0.0604 (mm) REVERT: F 247 LYS cc_start: 0.5796 (mttp) cc_final: 0.5177 (ttpp) outliers start: 66 outliers final: 28 residues processed: 253 average time/residue: 1.3806 time to fit residues: 387.8757 Evaluate side-chains 241 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 419 TYR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 184 optimal weight: 0.0670 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1197 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1447 ASN C 17 HIS E 69 GLN E 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.190548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137265 restraints weight = 20841.339| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.10 r_work: 0.3761 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17193 Z= 0.220 Angle : 0.611 9.900 23285 Z= 0.317 Chirality : 0.044 0.203 2368 Planarity : 0.006 0.114 2952 Dihedral : 4.886 32.282 2187 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 4.76 % Allowed : 21.46 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.16 (0.20), residues: 1940 helix: 1.19 (0.17), residues: 992 sheet: 1.05 (0.55), residues: 89 loop : -1.33 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 160 HIS 0.005 0.001 HIS C 63 PHE 0.028 0.002 PHE F 216 TYR 0.017 0.002 TYR F 177 ARG 0.016 0.001 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 206 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8188 (mm) cc_final: 0.7709 (tp) REVERT: A 47 ARG cc_start: 0.6816 (ttt90) cc_final: 0.5703 (ttp-170) REVERT: A 75 MET cc_start: 0.8577 (tpt) cc_final: 0.8112 (mmm) REVERT: A 111 HIS cc_start: 0.2873 (OUTLIER) cc_final: 0.2646 (t70) REVERT: A 125 MET cc_start: 0.5401 (mpp) cc_final: 0.4026 (mtt) REVERT: A 185 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.5062 (p90) REVERT: A 186 MET cc_start: 0.5561 (mtm) cc_final: 0.4882 (mtt) REVERT: A 238 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 494 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7092 (mtm180) REVERT: A 622 ASN cc_start: 0.1570 (OUTLIER) cc_final: 0.1224 (m110) REVERT: A 668 MET cc_start: 0.3955 (OUTLIER) cc_final: 0.2834 (ptm) REVERT: A 672 ARG cc_start: 0.4470 (OUTLIER) cc_final: 0.2913 (tpp80) REVERT: A 701 PHE cc_start: 0.7558 (m-10) cc_final: 0.7255 (m-80) REVERT: A 1144 MET cc_start: 0.4126 (tpp) cc_final: 0.3420 (ttm) REVERT: A 1185 PHE cc_start: 0.6261 (t80) cc_final: 0.5804 (t80) REVERT: A 1193 PHE cc_start: 0.7552 (t80) cc_final: 0.7304 (t80) REVERT: A 1225 TYR cc_start: 0.8105 (t80) cc_final: 0.7814 (t80) REVERT: A 1605 MET cc_start: 0.4211 (tmm) cc_final: 0.3563 (mmm) REVERT: A 1737 LYS cc_start: 0.6692 (tttp) cc_final: 0.5869 (pmtt) REVERT: B 116 MET cc_start: 0.1819 (tpp) cc_final: 0.1250 (mtm) REVERT: B 157 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6136 (tt0) REVERT: B 158 PHE cc_start: 0.6238 (m-80) cc_final: 0.6023 (m-10) REVERT: B 167 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5526 (mp) REVERT: B 179 PHE cc_start: 0.3985 (t80) cc_final: 0.3199 (m-80) REVERT: B 204 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5439 (tmm) REVERT: B 218 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.6259 (mtmp) REVERT: B 271 ILE cc_start: 0.5192 (OUTLIER) cc_final: 0.4713 (tt) REVERT: C 97 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: D 282 ARG cc_start: 0.6940 (mtp180) cc_final: 0.6675 (mtp180) REVERT: D 452 GLN cc_start: 0.8525 (tt0) cc_final: 0.8308 (mt0) REVERT: D 455 GLU cc_start: 0.8797 (tp30) cc_final: 0.8210 (tp30) REVERT: D 528 LYS cc_start: 0.7047 (mtmm) cc_final: 0.6640 (ttmm) REVERT: D 533 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7578 (pp) REVERT: E 73 GLN cc_start: 0.7250 (tp-100) cc_final: 0.6689 (tp40) REVERT: E 142 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7963 (ttpt) REVERT: E 144 GLU cc_start: 0.7822 (tp30) cc_final: 0.7539 (tt0) REVERT: E 227 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8102 (ttpp) REVERT: E 419 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: E 443 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7301 (mtm110) REVERT: F 181 ILE cc_start: 0.1027 (OUTLIER) cc_final: 0.0713 (mm) REVERT: F 247 LYS cc_start: 0.5775 (mttp) cc_final: 0.5149 (ttpp) outliers start: 85 outliers final: 34 residues processed: 265 average time/residue: 1.3458 time to fit residues: 397.0243 Evaluate side-chains 246 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 419 TYR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 158 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 ASN ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN C 17 HIS C 51 ASN E 69 GLN E 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.193043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139218 restraints weight = 20769.501| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.15 r_work: 0.3798 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17193 Z= 0.171 Angle : 0.585 11.153 23285 Z= 0.301 Chirality : 0.043 0.218 2368 Planarity : 0.005 0.089 2952 Dihedral : 4.720 31.499 2187 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 4.20 % Allowed : 22.07 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.31 (0.20), residues: 1940 helix: 1.37 (0.17), residues: 986 sheet: 1.06 (0.55), residues: 89 loop : -1.29 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 123 HIS 0.005 0.001 HIS C 63 PHE 0.028 0.001 PHE F 216 TYR 0.027 0.001 TYR F 226 ARG 0.013 0.000 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 1.897 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8231 (mm) cc_final: 0.7720 (tp) REVERT: A 47 ARG cc_start: 0.6966 (ttt90) cc_final: 0.5802 (ttp-170) REVERT: A 75 MET cc_start: 0.8554 (tpt) cc_final: 0.8148 (mmm) REVERT: A 111 HIS cc_start: 0.2830 (OUTLIER) cc_final: 0.2354 (t70) REVERT: A 185 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.5213 (p90) REVERT: A 186 MET cc_start: 0.5650 (mtm) cc_final: 0.4951 (mtt) REVERT: A 426 PHE cc_start: 0.3885 (OUTLIER) cc_final: 0.3407 (m-80) REVERT: A 494 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6922 (mtm180) REVERT: A 622 ASN cc_start: 0.1362 (OUTLIER) cc_final: -0.0116 (m-40) REVERT: A 668 MET cc_start: 0.3812 (OUTLIER) cc_final: 0.3231 (ptt) REVERT: A 672 ARG cc_start: 0.4162 (OUTLIER) cc_final: 0.2895 (ppp80) REVERT: A 701 PHE cc_start: 0.7545 (m-10) cc_final: 0.7249 (m-80) REVERT: A 1144 MET cc_start: 0.4346 (tpp) cc_final: 0.3424 (ttm) REVERT: A 1185 PHE cc_start: 0.6140 (t80) cc_final: 0.5739 (t80) REVERT: A 1193 PHE cc_start: 0.7476 (t80) cc_final: 0.7212 (t80) REVERT: A 1225 TYR cc_start: 0.8082 (t80) cc_final: 0.7807 (t80) REVERT: A 1447 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6969 (m110) REVERT: A 1605 MET cc_start: 0.4125 (tmm) cc_final: 0.3531 (mmm) REVERT: A 1737 LYS cc_start: 0.6741 (tttp) cc_final: 0.5927 (pmtt) REVERT: B 116 MET cc_start: 0.1605 (tpp) cc_final: 0.1198 (mtm) REVERT: B 157 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.6042 (tt0) REVERT: B 179 PHE cc_start: 0.3900 (t80) cc_final: 0.3044 (m-80) REVERT: B 195 PHE cc_start: 0.4622 (t80) cc_final: 0.4391 (t80) REVERT: B 204 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5402 (tmm) REVERT: B 218 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.6238 (mtmp) REVERT: B 229 PHE cc_start: 0.8084 (t80) cc_final: 0.7713 (t80) REVERT: B 260 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6349 (pt) REVERT: C 97 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: D 282 ARG cc_start: 0.6887 (mtp180) cc_final: 0.6629 (mtp180) REVERT: D 353 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 388 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8082 (mm-30) REVERT: D 452 GLN cc_start: 0.8523 (tt0) cc_final: 0.8290 (mt0) REVERT: D 455 GLU cc_start: 0.8798 (tp30) cc_final: 0.8222 (tp30) REVERT: D 528 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6736 (ttmm) REVERT: D 533 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7397 (pp) REVERT: E 73 GLN cc_start: 0.7243 (tp-100) cc_final: 0.6671 (tp40) REVERT: E 122 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7144 (mtm180) REVERT: E 142 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7925 (ttpt) REVERT: E 144 GLU cc_start: 0.7739 (tp30) cc_final: 0.7434 (tt0) REVERT: E 227 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8018 (ttpp) REVERT: E 419 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.5904 (m-80) REVERT: E 443 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7239 (mtm110) REVERT: F 181 ILE cc_start: 0.0957 (OUTLIER) cc_final: 0.0645 (mm) REVERT: F 247 LYS cc_start: 0.5806 (mttp) cc_final: 0.5194 (ttpp) outliers start: 75 outliers final: 28 residues processed: 250 average time/residue: 1.3595 time to fit residues: 376.9623 Evaluate side-chains 237 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 419 TYR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 151 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1197 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1447 ASN C 17 HIS E 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.191322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137454 restraints weight = 20547.957| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.12 r_work: 0.3780 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17193 Z= 0.197 Angle : 0.597 9.850 23285 Z= 0.309 Chirality : 0.043 0.217 2368 Planarity : 0.006 0.174 2952 Dihedral : 4.746 31.238 2187 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.40 % Rotamer: Outliers : 4.20 % Allowed : 22.13 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.29 (0.20), residues: 1940 helix: 1.33 (0.17), residues: 992 sheet: 1.10 (0.55), residues: 89 loop : -1.30 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 123 HIS 0.004 0.001 HIS C 63 PHE 0.045 0.002 PHE D 461 TYR 0.016 0.001 TYR F 177 ARG 0.018 0.000 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 197 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8229 (mm) cc_final: 0.7719 (tp) REVERT: A 47 ARG cc_start: 0.6983 (ttt90) cc_final: 0.5801 (ttp-170) REVERT: A 75 MET cc_start: 0.8565 (tpt) cc_final: 0.8164 (mmm) REVERT: A 111 HIS cc_start: 0.2618 (OUTLIER) cc_final: 0.2195 (t70) REVERT: A 185 PHE cc_start: 0.5889 (OUTLIER) cc_final: 0.5134 (p90) REVERT: A 186 MET cc_start: 0.5664 (mtm) cc_final: 0.4949 (mtt) REVERT: A 238 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6220 (t80) REVERT: A 494 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7052 (mtm180) REVERT: A 622 ASN cc_start: 0.1489 (OUTLIER) cc_final: -0.0001 (m-40) REVERT: A 668 MET cc_start: 0.3897 (OUTLIER) cc_final: 0.3356 (ptt) REVERT: A 672 ARG cc_start: 0.4213 (OUTLIER) cc_final: 0.2920 (ppp80) REVERT: A 701 PHE cc_start: 0.7545 (m-10) cc_final: 0.7253 (m-80) REVERT: A 1144 MET cc_start: 0.4291 (tpp) cc_final: 0.3382 (ttm) REVERT: A 1185 PHE cc_start: 0.6193 (t80) cc_final: 0.5622 (t80) REVERT: A 1225 TYR cc_start: 0.8083 (t80) cc_final: 0.7802 (t80) REVERT: A 1605 MET cc_start: 0.4272 (tmm) cc_final: 0.3710 (mmm) REVERT: A 1737 LYS cc_start: 0.6761 (tttp) cc_final: 0.5949 (pmtt) REVERT: B 116 MET cc_start: 0.1528 (tpp) cc_final: 0.1147 (mtm) REVERT: B 157 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6041 (tt0) REVERT: B 167 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5370 (mp) REVERT: B 179 PHE cc_start: 0.3816 (t80) cc_final: 0.2882 (m-80) REVERT: B 195 PHE cc_start: 0.4647 (t80) cc_final: 0.4424 (t80) REVERT: B 204 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5432 (tmm) REVERT: B 229 PHE cc_start: 0.8048 (t80) cc_final: 0.7720 (t80) REVERT: B 260 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6378 (pt) REVERT: C 97 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: D 282 ARG cc_start: 0.6865 (mtp180) cc_final: 0.6602 (mtp180) REVERT: D 353 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7564 (mt-10) REVERT: D 388 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8050 (mm-30) REVERT: D 452 GLN cc_start: 0.8513 (tt0) cc_final: 0.8281 (mt0) REVERT: D 455 GLU cc_start: 0.8796 (tp30) cc_final: 0.8211 (tp30) REVERT: D 473 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: D 533 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7426 (pp) REVERT: E 142 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7999 (ttpt) REVERT: E 144 GLU cc_start: 0.7758 (tp30) cc_final: 0.7454 (tt0) REVERT: E 227 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8053 (ttpp) REVERT: E 419 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: E 443 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7239 (mtm110) REVERT: F 247 LYS cc_start: 0.5646 (mttp) cc_final: 0.5073 (ttpp) outliers start: 75 outliers final: 36 residues processed: 247 average time/residue: 1.3926 time to fit residues: 381.4994 Evaluate side-chains 243 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1447 ASN Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 419 TYR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 156 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.0070 chunk 52 optimal weight: 0.0870 chunk 195 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 182 optimal weight: 0.0980 chunk 54 optimal weight: 0.0470 overall best weight: 0.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1178 ASN ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 ASN C 17 HIS C 51 ASN E 69 GLN E 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.195652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.142705 restraints weight = 20701.101| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.12 r_work: 0.3849 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17193 Z= 0.152 Angle : 0.561 11.018 23285 Z= 0.290 Chirality : 0.042 0.218 2368 Planarity : 0.005 0.132 2952 Dihedral : 4.415 29.955 2185 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 3.19 % Allowed : 23.47 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.50 (0.20), residues: 1940 helix: 1.49 (0.17), residues: 997 sheet: 1.21 (0.55), residues: 89 loop : -1.20 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 123 HIS 0.004 0.001 HIS C 63 PHE 0.032 0.001 PHE A1193 TYR 0.017 0.001 TYR F 177 ARG 0.016 0.000 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8154 (mm) cc_final: 0.7731 (tp) REVERT: A 47 ARG cc_start: 0.6660 (ttt90) cc_final: 0.5442 (ttp-170) REVERT: A 51 MET cc_start: 0.4876 (mmp) cc_final: 0.4024 (ptm) REVERT: A 75 MET cc_start: 0.8497 (tpt) cc_final: 0.8061 (mmm) REVERT: A 111 HIS cc_start: 0.2701 (OUTLIER) cc_final: 0.2131 (t-90) REVERT: A 185 PHE cc_start: 0.5842 (OUTLIER) cc_final: 0.5233 (p90) REVERT: A 186 MET cc_start: 0.5485 (mtm) cc_final: 0.4846 (mtt) REVERT: A 238 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6212 (t80) REVERT: A 410 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: A 426 PHE cc_start: 0.4008 (OUTLIER) cc_final: 0.3493 (m-80) REVERT: A 494 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6587 (mtm180) REVERT: A 595 MET cc_start: 0.0616 (ppp) cc_final: -0.0852 (mmt) REVERT: A 622 ASN cc_start: 0.1025 (OUTLIER) cc_final: -0.0305 (m-40) REVERT: A 668 MET cc_start: 0.3825 (OUTLIER) cc_final: 0.3221 (ptt) REVERT: A 672 ARG cc_start: 0.3736 (OUTLIER) cc_final: 0.3245 (ppp80) REVERT: A 701 PHE cc_start: 0.7489 (m-10) cc_final: 0.7183 (m-80) REVERT: A 1144 MET cc_start: 0.4158 (tpp) cc_final: 0.3337 (ttm) REVERT: A 1185 PHE cc_start: 0.6062 (t80) cc_final: 0.5646 (t80) REVERT: A 1225 TYR cc_start: 0.7941 (t80) cc_final: 0.7718 (t80) REVERT: A 1281 SER cc_start: 0.5651 (OUTLIER) cc_final: 0.4556 (m) REVERT: A 1605 MET cc_start: 0.4027 (tmm) cc_final: 0.3561 (mmm) REVERT: A 1737 LYS cc_start: 0.6727 (tttp) cc_final: 0.5943 (pmtt) REVERT: B 167 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5205 (mp) REVERT: B 179 PHE cc_start: 0.3830 (t80) cc_final: 0.2888 (m-80) REVERT: B 191 GLU cc_start: 0.3224 (OUTLIER) cc_final: 0.2423 (pt0) REVERT: B 204 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.5173 (tmm) REVERT: B 218 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.6216 (mtmp) REVERT: B 229 PHE cc_start: 0.7932 (t80) cc_final: 0.7678 (t80) REVERT: B 260 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.6131 (pt) REVERT: C 97 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: D 353 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 388 GLU cc_start: 0.8209 (mm-30) cc_final: 0.8000 (mm-30) REVERT: D 452 GLN cc_start: 0.8496 (tt0) cc_final: 0.8252 (mt0) REVERT: D 455 GLU cc_start: 0.8772 (tp30) cc_final: 0.8128 (tp30) REVERT: D 473 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: E 73 GLN cc_start: 0.7127 (tp-100) cc_final: 0.6558 (tp40) REVERT: E 122 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7134 (mtm180) REVERT: E 142 LYS cc_start: 0.8158 (ttpp) cc_final: 0.7863 (ttpt) REVERT: E 144 GLU cc_start: 0.7572 (tp30) cc_final: 0.7299 (tt0) REVERT: E 227 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7886 (ttpp) REVERT: E 279 GLU cc_start: 0.7881 (pt0) cc_final: 0.7173 (pt0) REVERT: E 419 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: E 443 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7194 (mtm110) REVERT: F 181 ILE cc_start: 0.0655 (OUTLIER) cc_final: 0.0348 (mm) REVERT: F 220 MET cc_start: 0.1276 (mtm) cc_final: 0.0818 (mmm) REVERT: F 247 LYS cc_start: 0.5663 (mttp) cc_final: 0.5281 (ttpp) outliers start: 57 outliers final: 18 residues processed: 248 average time/residue: 1.4038 time to fit residues: 386.3949 Evaluate side-chains 234 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 1140 ASN Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 419 TYR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 183 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1178 ASN A1197 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.193497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139664 restraints weight = 20757.570| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.14 r_work: 0.3814 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17193 Z= 0.179 Angle : 0.587 11.226 23285 Z= 0.302 Chirality : 0.043 0.220 2368 Planarity : 0.006 0.160 2952 Dihedral : 4.449 29.012 2185 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.51 % Rotamer: Outliers : 2.75 % Allowed : 24.31 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.52 (0.20), residues: 1940 helix: 1.53 (0.17), residues: 987 sheet: 1.09 (0.56), residues: 90 loop : -1.18 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 123 HIS 0.006 0.001 HIS C 17 PHE 0.029 0.001 PHE F 216 TYR 0.025 0.001 TYR F 226 ARG 0.019 0.000 ARG A1761 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 2.135 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8176 (mm) cc_final: 0.7738 (tp) REVERT: A 47 ARG cc_start: 0.6778 (ttt90) cc_final: 0.5621 (ttp-170) REVERT: A 75 MET cc_start: 0.8510 (tpt) cc_final: 0.8095 (mmm) REVERT: A 111 HIS cc_start: 0.2764 (OUTLIER) cc_final: 0.2181 (t-90) REVERT: A 185 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5161 (p90) REVERT: A 186 MET cc_start: 0.5507 (mtm) cc_final: 0.4854 (mtt) REVERT: A 426 PHE cc_start: 0.4062 (OUTLIER) cc_final: 0.3600 (m-80) REVERT: A 494 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7052 (mtm180) REVERT: A 622 ASN cc_start: 0.0802 (OUTLIER) cc_final: -0.0407 (m-40) REVERT: A 668 MET cc_start: 0.3894 (OUTLIER) cc_final: 0.3323 (ptt) REVERT: A 672 ARG cc_start: 0.3919 (OUTLIER) cc_final: 0.3257 (ppp80) REVERT: A 701 PHE cc_start: 0.7522 (m-10) cc_final: 0.7216 (m-80) REVERT: A 1144 MET cc_start: 0.4098 (tpp) cc_final: 0.3322 (ttm) REVERT: A 1185 PHE cc_start: 0.6086 (t80) cc_final: 0.5580 (t80) REVERT: A 1225 TYR cc_start: 0.7974 (t80) cc_final: 0.7726 (t80) REVERT: A 1281 SER cc_start: 0.5676 (OUTLIER) cc_final: 0.4583 (m) REVERT: A 1605 MET cc_start: 0.3994 (tmm) cc_final: 0.3560 (mmm) REVERT: A 1737 LYS cc_start: 0.6732 (tttp) cc_final: 0.5944 (pmtt) REVERT: B 116 MET cc_start: 0.2563 (OUTLIER) cc_final: 0.2284 (mtt) REVERT: B 144 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: B 167 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5248 (mp) REVERT: B 179 PHE cc_start: 0.3836 (t80) cc_final: 0.2888 (m-80) REVERT: B 191 GLU cc_start: 0.3242 (OUTLIER) cc_final: 0.2461 (pt0) REVERT: B 204 MET cc_start: 0.5501 (OUTLIER) cc_final: 0.5197 (tmm) REVERT: B 218 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6234 (mtmp) REVERT: B 229 PHE cc_start: 0.7956 (t80) cc_final: 0.7729 (t80) REVERT: B 260 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6329 (pt) REVERT: C 97 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: D 353 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 388 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8112 (mm-30) REVERT: D 452 GLN cc_start: 0.8512 (tt0) cc_final: 0.8279 (mt0) REVERT: D 455 GLU cc_start: 0.8799 (tp30) cc_final: 0.8164 (tp30) REVERT: D 473 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: D 528 LYS cc_start: 0.7264 (mtmm) cc_final: 0.6882 (ttmm) REVERT: E 122 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7198 (mtm180) REVERT: E 142 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7923 (ttpt) REVERT: E 144 GLU cc_start: 0.7665 (tp30) cc_final: 0.7369 (tt0) REVERT: E 227 LYS cc_start: 0.8340 (ttpp) cc_final: 0.7941 (ttpp) REVERT: E 279 GLU cc_start: 0.7599 (pt0) cc_final: 0.7223 (pt0) REVERT: E 419 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.5630 (m-80) REVERT: E 443 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7197 (mtm110) REVERT: F 220 MET cc_start: 0.1283 (mtm) cc_final: 0.0818 (mmm) REVERT: F 247 LYS cc_start: 0.5878 (mttp) cc_final: 0.5288 (ttpp) outliers start: 49 outliers final: 18 residues processed: 233 average time/residue: 1.3887 time to fit residues: 359.0448 Evaluate side-chains 236 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1779 MET Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 419 TYR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 65 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1197 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN E 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.192949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138925 restraints weight = 20746.273| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.14 r_work: 0.3804 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17193 Z= 0.188 Angle : 0.606 11.278 23285 Z= 0.312 Chirality : 0.044 0.316 2368 Planarity : 0.006 0.151 2952 Dihedral : 4.531 29.931 2185 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.30 % Rotamer: Outliers : 2.69 % Allowed : 24.54 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.47 (0.20), residues: 1940 helix: 1.47 (0.17), residues: 994 sheet: 1.08 (0.55), residues: 90 loop : -1.22 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 123 HIS 0.005 0.001 HIS C 63 PHE 0.029 0.001 PHE F 216 TYR 0.015 0.001 TYR F 177 ARG 0.018 0.000 ARG A1761 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8174 (mm) cc_final: 0.7721 (tp) REVERT: A 47 ARG cc_start: 0.6792 (ttt90) cc_final: 0.5663 (ttp-170) REVERT: A 51 MET cc_start: 0.4580 (mmp) cc_final: 0.3773 (ptm) REVERT: A 75 MET cc_start: 0.8527 (tpt) cc_final: 0.8125 (mmm) REVERT: A 111 HIS cc_start: 0.2794 (OUTLIER) cc_final: 0.2168 (t-90) REVERT: A 185 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.5115 (p90) REVERT: A 186 MET cc_start: 0.5543 (mtm) cc_final: 0.4908 (mtt) REVERT: A 426 PHE cc_start: 0.4196 (OUTLIER) cc_final: 0.3740 (m-80) REVERT: A 494 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7037 (mtm180) REVERT: A 622 ASN cc_start: 0.1267 (OUTLIER) cc_final: -0.0047 (m-40) REVERT: A 668 MET cc_start: 0.3901 (OUTLIER) cc_final: 0.3339 (ptt) REVERT: A 672 ARG cc_start: 0.3985 (OUTLIER) cc_final: 0.3273 (ppp80) REVERT: A 701 PHE cc_start: 0.7512 (m-10) cc_final: 0.7215 (m-80) REVERT: A 1144 MET cc_start: 0.3984 (tpp) cc_final: 0.3286 (ttm) REVERT: A 1168 PHE cc_start: 0.4348 (OUTLIER) cc_final: 0.4133 (p90) REVERT: A 1185 PHE cc_start: 0.6153 (t80) cc_final: 0.5682 (t80) REVERT: A 1225 TYR cc_start: 0.7974 (t80) cc_final: 0.7722 (t80) REVERT: A 1281 SER cc_start: 0.5741 (OUTLIER) cc_final: 0.4656 (m) REVERT: A 1605 MET cc_start: 0.3926 (tmm) cc_final: 0.3510 (mmm) REVERT: A 1737 LYS cc_start: 0.6724 (tttp) cc_final: 0.5938 (pmtt) REVERT: B 116 MET cc_start: 0.2570 (OUTLIER) cc_final: 0.2277 (mtt) REVERT: B 144 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: B 167 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5229 (mp) REVERT: B 179 PHE cc_start: 0.3823 (t80) cc_final: 0.2873 (m-80) REVERT: B 191 GLU cc_start: 0.3199 (OUTLIER) cc_final: 0.2481 (pt0) REVERT: B 195 PHE cc_start: 0.4778 (t80) cc_final: 0.4511 (t80) REVERT: B 204 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5361 (tmm) REVERT: B 218 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6254 (mtmp) REVERT: B 229 PHE cc_start: 0.8029 (t80) cc_final: 0.7685 (t80) REVERT: B 260 ILE cc_start: 0.6625 (OUTLIER) cc_final: 0.6418 (pt) REVERT: C 97 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: D 353 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7563 (mt-10) REVERT: D 388 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8071 (mm-30) REVERT: D 452 GLN cc_start: 0.8509 (tt0) cc_final: 0.8260 (mt0) REVERT: D 455 GLU cc_start: 0.8788 (tp30) cc_final: 0.8154 (tp30) REVERT: D 473 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: D 528 LYS cc_start: 0.7295 (mtmm) cc_final: 0.6905 (ttmm) REVERT: E 142 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7945 (ttpt) REVERT: E 144 GLU cc_start: 0.7688 (tp30) cc_final: 0.7410 (tt0) REVERT: E 227 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7983 (ttpp) REVERT: E 279 GLU cc_start: 0.7441 (pt0) cc_final: 0.7178 (pt0) REVERT: E 419 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: E 443 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7197 (mtm110) REVERT: F 220 MET cc_start: 0.1469 (mtm) cc_final: 0.0763 (mmm) REVERT: F 247 LYS cc_start: 0.5619 (mttp) cc_final: 0.5108 (ttpp) outliers start: 48 outliers final: 21 residues processed: 234 average time/residue: 1.3917 time to fit residues: 361.9956 Evaluate side-chains 240 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1168 PHE Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1779 MET Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 419 TYR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 193 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 0.0060 chunk 174 optimal weight: 0.6980 chunk 190 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 121 optimal weight: 0.0470 chunk 80 optimal weight: 7.9990 chunk 135 optimal weight: 0.0170 chunk 70 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1197 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN E 95 ASN E 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.195295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141646 restraints weight = 20783.736| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.15 r_work: 0.3825 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17193 Z= 0.164 Angle : 0.588 12.274 23285 Z= 0.300 Chirality : 0.043 0.343 2368 Planarity : 0.007 0.230 2952 Dihedral : 4.435 29.310 2185 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 2.18 % Allowed : 24.99 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.54 (0.20), residues: 1940 helix: 1.55 (0.17), residues: 989 sheet: 1.10 (0.55), residues: 90 loop : -1.18 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 123 HIS 0.005 0.001 HIS C 63 PHE 0.033 0.001 PHE D 461 TYR 0.017 0.001 TYR B 178 ARG 0.013 0.000 ARG A1761 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15899.98 seconds wall clock time: 280 minutes 14.86 seconds (16814.86 seconds total)