Starting phenix.real_space_refine on Tue Dec 31 21:15:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9y_39872/12_2024/8z9y_39872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9y_39872/12_2024/8z9y_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_39872/12_2024/8z9y_39872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9y_39872/12_2024/8z9y_39872.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9y_39872/12_2024/8z9y_39872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9y_39872/12_2024/8z9y_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-5532/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: 11.52, per 1000 atoms: 0.69 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: 4.37 Conformation dependent library (CDL) restraints added in 2.3 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: 1.69 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: 5.08 Time building geometry restraints manager: 5.03 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: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 0.630 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 39.200 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- 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 : 1.942 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: 1.4870 time to fit residues: 394.2879 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 : 2.133 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.6712 (tpt) cc_final: 0.6392 (tpt) REVERT: A 20 ILE cc_start: 0.7721 (mm) cc_final: 0.7434 (tp) REVERT: A 75 MET cc_start: 0.8315 (tpt) cc_final: 0.7952 (mmm) REVERT: A 125 MET cc_start: 0.5250 (mpp) cc_final: 0.3779 (mtt) REVERT: A 129 ARG cc_start: 0.5473 (tpt90) cc_final: 0.5225 (tpt90) REVERT: A 186 MET cc_start: 0.5182 (mtm) cc_final: 0.4650 (mtt) REVERT: A 494 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6827 (mtm180) REVERT: A 668 MET cc_start: 0.3983 (pmm) cc_final: 0.3240 (ptm) REVERT: A 701 PHE cc_start: 0.7098 (m-10) cc_final: 0.6881 (m-80) REVERT: A 1185 PHE cc_start: 0.5966 (t80) cc_final: 0.5574 (t80) REVERT: A 1193 PHE cc_start: 0.7486 (t80) cc_final: 0.7238 (t80) REVERT: A 1225 TYR cc_start: 0.8155 (t80) cc_final: 0.7804 (t80) REVERT: A 1605 MET cc_start: 0.4086 (tmm) cc_final: 0.3467 (mmm) REVERT: A 1689 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7526 (tptm) REVERT: A 1737 LYS cc_start: 0.6391 (tttp) cc_final: 0.5568 (pmtt) REVERT: B 116 MET cc_start: 0.1784 (tpp) cc_final: 0.0997 (mtp) REVERT: B 179 PHE cc_start: 0.3200 (t80) cc_final: 0.2447 (m-80) REVERT: B 204 MET cc_start: 0.5607 (OUTLIER) cc_final: 0.4953 (tmm) REVERT: D 125 GLN cc_start: 0.7731 (mp10) cc_final: 0.7454 (mp10) REVERT: D 165 ASP cc_start: 0.7975 (t70) cc_final: 0.7463 (t70) REVERT: D 259 ASP cc_start: 0.7682 (m-30) cc_final: 0.7264 (m-30) REVERT: D 282 ARG cc_start: 0.6897 (mtp180) cc_final: 0.6618 (mtp180) REVERT: D 288 TYR cc_start: 0.8657 (m-80) cc_final: 0.8222 (m-80) REVERT: D 388 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7947 (mm-30) REVERT: D 452 GLN cc_start: 0.8282 (tt0) cc_final: 0.7904 (mt0) REVERT: D 455 GLU cc_start: 0.8373 (tp30) cc_final: 0.7643 (tp30) REVERT: D 528 LYS cc_start: 0.7190 (mtmm) cc_final: 0.6806 (ttmm) REVERT: E 73 GLN cc_start: 0.6679 (tp-100) cc_final: 0.5988 (tp40) REVERT: E 122 ARG cc_start: 0.6932 (mtm110) cc_final: 0.6204 (mtm180) REVERT: E 142 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7454 (ttpt) REVERT: E 144 GLU cc_start: 0.7333 (tp30) cc_final: 0.6893 (tt0) REVERT: E 227 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7649 (ttpp) REVERT: E 331 GLN cc_start: 0.7973 (mt0) cc_final: 0.7759 (mt0) REVERT: E 350 ASN cc_start: 0.8581 (t0) cc_final: 0.8301 (t0) REVERT: E 443 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6781 (mtm110) REVERT: F 247 LYS cc_start: 0.4611 (mttp) cc_final: 0.4196 (ttpp) outliers start: 50 outliers final: 20 residues processed: 248 average time/residue: 1.4990 time to fit residues: 411.8850 Evaluate side-chains 227 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 A residue 1689 LYS 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 98 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 0.0020 chunk 176 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 overall best weight: 0.7148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1447 ASN C 51 ASN E 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17193 Z= 0.193 Angle : 0.590 10.359 23285 Z= 0.305 Chirality : 0.044 0.202 2368 Planarity : 0.006 0.150 2952 Dihedral : 4.745 30.711 2187 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.40 % Rotamer: Outliers : 3.64 % Allowed : 21.12 % Favored : 75.24 % 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: 0.45 (0.20), residues: 1940 helix: 1.43 (0.17), residues: 997 sheet: 1.09 (0.56), residues: 89 loop : -1.18 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 123 HIS 0.005 0.001 HIS C 63 PHE 0.029 0.002 PHE F 173 TYR 0.028 0.001 TYR F 226 ARG 0.007 0.000 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 278 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.6808 (tpt) cc_final: 0.6447 (tpt) REVERT: A 20 ILE cc_start: 0.7679 (mm) cc_final: 0.7371 (tp) REVERT: A 47 ARG cc_start: 0.6492 (ttt90) cc_final: 0.5173 (ttp-170) REVERT: A 75 MET cc_start: 0.8292 (tpt) cc_final: 0.7894 (mmm) REVERT: A 161 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8368 (mtm) REVERT: A 185 PHE cc_start: 0.5799 (OUTLIER) cc_final: 0.4730 (p90) REVERT: A 186 MET cc_start: 0.5189 (mtm) cc_final: 0.4555 (mtt) REVERT: A 410 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: A 494 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6740 (mtm180) REVERT: A 622 ASN cc_start: 0.1145 (OUTLIER) cc_final: -0.0049 (m-40) REVERT: A 668 MET cc_start: 0.4078 (OUTLIER) cc_final: 0.3186 (ptm) REVERT: A 672 ARG cc_start: 0.3771 (OUTLIER) cc_final: 0.2479 (tpp80) REVERT: A 701 PHE cc_start: 0.7122 (m-10) cc_final: 0.6851 (m-80) REVERT: A 1144 MET cc_start: 0.4420 (tpp) cc_final: 0.3544 (ttm) REVERT: A 1185 PHE cc_start: 0.6091 (t80) cc_final: 0.5597 (t80) REVERT: A 1193 PHE cc_start: 0.7638 (t80) cc_final: 0.7320 (t80) REVERT: A 1225 TYR cc_start: 0.8057 (t80) cc_final: 0.7753 (t80) REVERT: A 1534 GLU cc_start: 0.4704 (OUTLIER) cc_final: 0.4493 (mm-30) REVERT: A 1605 MET cc_start: 0.4229 (tmm) cc_final: 0.3436 (mmm) REVERT: A 1689 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7469 (tptm) REVERT: A 1737 LYS cc_start: 0.6307 (tttp) cc_final: 0.5508 (pmtt) REVERT: B 116 MET cc_start: 0.1695 (tpp) cc_final: 0.1171 (mtt) REVERT: B 161 TYR cc_start: 0.5300 (m-10) cc_final: 0.4783 (m-10) REVERT: B 179 PHE cc_start: 0.3263 (t80) cc_final: 0.2584 (m-80) REVERT: B 195 PHE cc_start: 0.4276 (t80) cc_final: 0.3999 (t80) REVERT: B 204 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4893 (tmm) REVERT: B 218 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5629 (mtmp) REVERT: B 229 PHE cc_start: 0.7622 (t80) cc_final: 0.7195 (t80) REVERT: B 271 ILE cc_start: 0.5082 (OUTLIER) cc_final: 0.4721 (tt) REVERT: C 97 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: D 110 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: D 125 GLN cc_start: 0.7708 (mp10) cc_final: 0.7445 (mp10) REVERT: D 282 ARG cc_start: 0.6843 (mtp180) cc_final: 0.6519 (mtp180) REVERT: D 288 TYR cc_start: 0.8718 (m-80) cc_final: 0.8326 (m-80) REVERT: D 388 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7886 (mm-30) REVERT: D 452 GLN cc_start: 0.8216 (tt0) cc_final: 0.7853 (mt0) REVERT: D 455 GLU cc_start: 0.8389 (tp30) cc_final: 0.7642 (tp30) REVERT: D 528 LYS cc_start: 0.7203 (mtmm) cc_final: 0.6847 (ttmm) REVERT: E 73 GLN cc_start: 0.6675 (tp-100) cc_final: 0.5833 (tp-100) REVERT: E 122 ARG cc_start: 0.7019 (mtm110) cc_final: 0.6740 (mtm110) REVERT: E 142 LYS cc_start: 0.7735 (ttpp) cc_final: 0.7421 (ttpt) REVERT: E 227 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7628 (ttpp) REVERT: E 350 ASN cc_start: 0.8563 (t0) cc_final: 0.8289 (t0) REVERT: E 419 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: E 443 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6753 (mtm110) REVERT: F 247 LYS cc_start: 0.4637 (mttp) cc_final: 0.4250 (ttpp) outliers start: 65 outliers final: 28 residues processed: 252 average time/residue: 1.3909 time to fit residues: 388.7969 Evaluate side-chains 246 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 161 MET Chi-restraints excluded: chain A residue 185 PHE 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 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 1146 TYR Chi-restraints excluded: chain A residue 1186 VAL 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 1534 GLU Chi-restraints excluded: chain A residue 1689 LYS Chi-restraints excluded: chain B residue 180 PHE 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 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 110 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 558 ASP 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 193 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 B 194 HIS C 17 HIS C 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 17193 Z= 0.329 Angle : 0.674 9.506 23285 Z= 0.351 Chirality : 0.047 0.202 2368 Planarity : 0.007 0.246 2952 Dihedral : 5.122 32.641 2187 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 4.26 % Allowed : 21.12 % Favored : 74.62 % 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: 0.07 (0.20), residues: 1940 helix: 1.12 (0.17), residues: 991 sheet: 1.03 (0.55), residues: 89 loop : -1.36 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 160 HIS 0.006 0.001 HIS A 105 PHE 0.028 0.002 PHE D 461 TYR 0.021 0.002 TYR A 480 ARG 0.019 0.001 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 287 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 211 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7040 (tpt) cc_final: 0.6745 (tpt) REVERT: A 20 ILE cc_start: 0.7817 (mm) cc_final: 0.7412 (tp) REVERT: A 75 MET cc_start: 0.8410 (tpt) cc_final: 0.7915 (mmm) REVERT: A 186 MET cc_start: 0.5430 (mtm) cc_final: 0.4827 (mtt) REVERT: A 410 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 494 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6893 (mtm180) REVERT: A 668 MET cc_start: 0.4104 (OUTLIER) cc_final: 0.3106 (ptm) REVERT: A 672 ARG cc_start: 0.3932 (OUTLIER) cc_final: 0.2587 (tpp80) REVERT: A 701 PHE cc_start: 0.7135 (m-10) cc_final: 0.6881 (m-80) REVERT: A 1185 PHE cc_start: 0.6370 (t80) cc_final: 0.5799 (t80) REVERT: A 1193 PHE cc_start: 0.7611 (t80) cc_final: 0.7338 (t80) REVERT: A 1225 TYR cc_start: 0.8076 (t80) cc_final: 0.7727 (t80) REVERT: A 1447 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.6940 (m110) REVERT: A 1605 MET cc_start: 0.4258 (tmm) cc_final: 0.3503 (mmm) REVERT: A 1737 LYS cc_start: 0.6350 (tttp) cc_final: 0.5536 (pmtt) REVERT: B 116 MET cc_start: 0.1794 (tpp) cc_final: 0.1229 (mtm) REVERT: B 161 TYR cc_start: 0.5251 (m-10) cc_final: 0.4743 (m-10) REVERT: B 179 PHE cc_start: 0.3362 (t80) cc_final: 0.2607 (m-80) REVERT: B 204 MET cc_start: 0.5686 (OUTLIER) cc_final: 0.5157 (tmm) REVERT: B 271 ILE cc_start: 0.4968 (OUTLIER) cc_final: 0.4571 (tt) REVERT: C 97 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: D 110 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: D 125 GLN cc_start: 0.7751 (mp10) cc_final: 0.7521 (mp10) REVERT: D 282 ARG cc_start: 0.6866 (mtp180) cc_final: 0.6527 (mtp180) REVERT: D 288 TYR cc_start: 0.8688 (m-80) cc_final: 0.8237 (m-80) REVERT: D 452 GLN cc_start: 0.8259 (tt0) cc_final: 0.7915 (mt0) REVERT: D 455 GLU cc_start: 0.8413 (tp30) cc_final: 0.7703 (tp30) REVERT: D 520 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5620 (tp) REVERT: D 528 LYS cc_start: 0.7170 (mtmm) cc_final: 0.6822 (ttmm) REVERT: D 533 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7046 (pp) REVERT: E 73 GLN cc_start: 0.6793 (tp-100) cc_final: 0.6028 (tp-100) REVERT: E 122 ARG cc_start: 0.7001 (mtm110) cc_final: 0.6737 (mtm110) REVERT: E 142 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7474 (ttpt) REVERT: E 144 GLU cc_start: 0.7450 (tp30) cc_final: 0.7006 (tt0) REVERT: E 227 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7651 (ttpp) REVERT: E 443 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6777 (mtm110) REVERT: F 247 LYS cc_start: 0.5170 (mttp) cc_final: 0.4693 (ttpp) outliers start: 76 outliers final: 36 residues processed: 262 average time/residue: 1.3623 time to fit residues: 396.7460 Evaluate side-chains 251 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 129 ARG Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 410 GLU 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 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 138 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 269 ILE Chi-restraints excluded: chain B residue 271 ILE 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 110 GLU 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 520 ILE 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 127 VAL Chi-restraints excluded: chain E residue 143 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 C 17 HIS C 51 ASN E 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17193 Z= 0.207 Angle : 0.609 11.010 23285 Z= 0.316 Chirality : 0.044 0.202 2368 Planarity : 0.006 0.137 2952 Dihedral : 4.901 32.499 2187 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.45 % Rotamer: Outliers : 3.98 % Allowed : 22.07 % Favored : 73.95 % 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: 0.18 (0.20), residues: 1940 helix: 1.23 (0.17), residues: 996 sheet: 1.00 (0.55), residues: 89 loop : -1.35 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 423 HIS 0.005 0.001 HIS C 63 PHE 0.028 0.002 PHE F 216 TYR 0.017 0.001 TYR F 177 ARG 0.019 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 281 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7832 (mm) cc_final: 0.7422 (tp) REVERT: A 47 ARG cc_start: 0.6360 (ttt90) cc_final: 0.5217 (ttp-170) REVERT: A 75 MET cc_start: 0.8383 (tpt) cc_final: 0.7956 (mmm) REVERT: A 111 HIS cc_start: 0.3026 (OUTLIER) cc_final: 0.2741 (t70) REVERT: A 186 MET cc_start: 0.5311 (mtm) cc_final: 0.4691 (mtt) REVERT: A 238 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.5995 (t80) REVERT: A 380 GLU cc_start: 0.6755 (pm20) cc_final: 0.6437 (pm20) REVERT: A 397 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8316 (mt) REVERT: A 410 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: A 494 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6901 (mtm180) REVERT: A 668 MET cc_start: 0.3888 (OUTLIER) cc_final: 0.2936 (ptm) REVERT: A 672 ARG cc_start: 0.3978 (OUTLIER) cc_final: 0.2667 (tpp80) REVERT: A 701 PHE cc_start: 0.7162 (m-10) cc_final: 0.6903 (m-80) REVERT: A 1144 MET cc_start: 0.4658 (tpp) cc_final: 0.3900 (ttm) REVERT: A 1185 PHE cc_start: 0.6292 (t80) cc_final: 0.5756 (t80) REVERT: A 1193 PHE cc_start: 0.7656 (t80) cc_final: 0.7324 (t80) REVERT: A 1225 TYR cc_start: 0.8052 (t80) cc_final: 0.7713 (t80) REVERT: A 1605 MET cc_start: 0.4065 (tmm) cc_final: 0.3409 (mmm) REVERT: A 1737 LYS cc_start: 0.6344 (tttp) cc_final: 0.5543 (pmtt) REVERT: B 116 MET cc_start: 0.1740 (tpp) cc_final: 0.1260 (mtm) REVERT: B 179 PHE cc_start: 0.3400 (t80) cc_final: 0.2632 (m-80) REVERT: B 204 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.5070 (tmm) REVERT: B 218 LYS cc_start: 0.5912 (OUTLIER) cc_final: 0.5687 (mtmp) REVERT: B 229 PHE cc_start: 0.7615 (t80) cc_final: 0.7255 (t80) REVERT: B 271 ILE cc_start: 0.4888 (OUTLIER) cc_final: 0.4493 (tt) REVERT: C 97 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: D 110 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: D 125 GLN cc_start: 0.7726 (mp10) cc_final: 0.7473 (mp10) REVERT: D 282 ARG cc_start: 0.6841 (mtp180) cc_final: 0.6512 (mtp180) REVERT: D 452 GLN cc_start: 0.8176 (tt0) cc_final: 0.7840 (mt0) REVERT: D 455 GLU cc_start: 0.8406 (tp30) cc_final: 0.7691 (tp30) REVERT: D 528 LYS cc_start: 0.7176 (mtmm) cc_final: 0.6822 (ttmm) REVERT: D 533 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6990 (pp) REVERT: E 97 ASP cc_start: 0.3921 (OUTLIER) cc_final: 0.3639 (p0) REVERT: E 122 ARG cc_start: 0.7163 (mtm110) cc_final: 0.6953 (mtm110) REVERT: E 142 LYS cc_start: 0.7750 (ttpp) cc_final: 0.7399 (ttpt) REVERT: E 144 GLU cc_start: 0.7356 (tp30) cc_final: 0.6996 (tt0) REVERT: E 227 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7631 (ttpp) REVERT: E 419 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6118 (m-80) REVERT: E 443 ARG cc_start: 0.7054 (mtm-85) cc_final: 0.6736 (mtm110) REVERT: F 247 LYS cc_start: 0.5139 (mttp) cc_final: 0.4671 (ttpp) outliers start: 71 outliers final: 33 residues processed: 254 average time/residue: 1.3736 time to fit residues: 388.3928 Evaluate side-chains 249 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 3.205 ------------------------------------------------------------------------------- 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 222 ASN Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 410 GLU 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 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 1700 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 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 95 VAL Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 110 GLU 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 97 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 127 VAL 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 63 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 A1447 ASN C 17 HIS E 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17193 Z= 0.228 Angle : 0.616 10.008 23285 Z= 0.320 Chirality : 0.044 0.211 2368 Planarity : 0.006 0.166 2952 Dihedral : 4.907 32.442 2187 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 92.99 % Rotamer: Outliers : 4.82 % Allowed : 21.29 % Favored : 73.89 % 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: 0.15 (0.20), residues: 1940 helix: 1.20 (0.17), residues: 991 sheet: 1.00 (0.55), residues: 89 loop : -1.35 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 A 160 ARG 0.017 0.001 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 291 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 205 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7847 (mm) cc_final: 0.7416 (tp) REVERT: A 47 ARG cc_start: 0.6400 (ttt90) cc_final: 0.5218 (ttp-170) REVERT: A 75 MET cc_start: 0.8386 (tpt) cc_final: 0.7965 (mmm) REVERT: A 111 HIS cc_start: 0.3088 (OUTLIER) cc_final: 0.2572 (t70) REVERT: A 186 MET cc_start: 0.5336 (mtm) cc_final: 0.4729 (mtt) REVERT: A 191 LEU cc_start: 0.4593 (OUTLIER) cc_final: 0.4380 (mt) REVERT: A 238 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5996 (t80) REVERT: A 410 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 426 PHE cc_start: 0.3096 (OUTLIER) cc_final: 0.2756 (m-80) REVERT: A 494 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6889 (mtm180) REVERT: A 622 ASN cc_start: 0.1625 (OUTLIER) cc_final: 0.1231 (m110) REVERT: A 668 MET cc_start: 0.3742 (OUTLIER) cc_final: 0.3271 (ptt) REVERT: A 672 ARG cc_start: 0.3890 (OUTLIER) cc_final: 0.2568 (tpp80) REVERT: A 701 PHE cc_start: 0.7208 (m-10) cc_final: 0.6936 (m-80) REVERT: A 1144 MET cc_start: 0.4467 (tpp) cc_final: 0.3757 (ttm) REVERT: A 1185 PHE cc_start: 0.6340 (t80) cc_final: 0.5756 (t80) REVERT: A 1193 PHE cc_start: 0.7621 (t80) cc_final: 0.7341 (t80) REVERT: A 1225 TYR cc_start: 0.8063 (t80) cc_final: 0.7713 (t80) REVERT: A 1605 MET cc_start: 0.4104 (tmm) cc_final: 0.3520 (mmm) REVERT: A 1737 LYS cc_start: 0.6332 (tttp) cc_final: 0.5529 (pmtt) REVERT: B 179 PHE cc_start: 0.3435 (t80) cc_final: 0.2650 (m-80) REVERT: B 204 MET cc_start: 0.5642 (OUTLIER) cc_final: 0.5105 (tmm) REVERT: B 218 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5663 (mtmp) REVERT: C 97 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: D 110 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: D 125 GLN cc_start: 0.7773 (mp10) cc_final: 0.7514 (mp10) REVERT: D 157 ASN cc_start: 0.7970 (m-40) cc_final: 0.7655 (m110) REVERT: D 158 ASP cc_start: 0.7141 (m-30) cc_final: 0.6897 (m-30) REVERT: D 282 ARG cc_start: 0.6829 (mtp180) cc_final: 0.6496 (mtp180) REVERT: D 290 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7419 (p) REVERT: D 452 GLN cc_start: 0.8182 (tt0) cc_final: 0.7875 (mt0) REVERT: D 455 GLU cc_start: 0.8396 (tp30) cc_final: 0.7686 (tp30) REVERT: D 528 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6795 (ttmm) REVERT: D 532 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7138 (mmm160) REVERT: D 533 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7047 (pp) REVERT: E 97 ASP cc_start: 0.3974 (OUTLIER) cc_final: 0.3699 (p0) REVERT: E 122 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6597 (mtm180) REVERT: E 142 LYS cc_start: 0.7750 (ttpp) cc_final: 0.7407 (ttpt) REVERT: E 144 GLU cc_start: 0.7404 (tp30) cc_final: 0.7047 (tt0) REVERT: E 227 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7634 (ttpp) REVERT: E 419 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6071 (m-80) REVERT: E 443 ARG cc_start: 0.7082 (mtm-85) cc_final: 0.6766 (mtm110) REVERT: F 247 LYS cc_start: 0.4945 (mttp) cc_final: 0.4521 (ttpp) outliers start: 86 outliers final: 34 residues processed: 268 average time/residue: 1.3258 time to fit residues: 396.5366 Evaluate side-chains 254 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 426 PHE 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 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 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 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 110 GLU Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 532 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 127 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1447 ASN B 211 GLN C 17 HIS C 51 ASN E 69 GLN E 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17193 Z= 0.232 Angle : 0.620 10.601 23285 Z= 0.322 Chirality : 0.044 0.212 2368 Planarity : 0.006 0.156 2952 Dihedral : 4.848 32.526 2185 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 4.31 % Allowed : 22.02 % 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: 0.15 (0.20), residues: 1940 helix: 1.21 (0.17), residues: 991 sheet: 1.00 (0.55), residues: 89 loop : -1.35 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 160 HIS 0.005 0.001 HIS C 63 PHE 0.028 0.002 PHE F 216 TYR 0.027 0.002 TYR F 226 ARG 0.019 0.001 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 280 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 203 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7849 (mm) cc_final: 0.7422 (tp) REVERT: A 47 ARG cc_start: 0.6402 (ttt90) cc_final: 0.5217 (ttp-170) REVERT: A 75 MET cc_start: 0.8383 (tpt) cc_final: 0.7969 (mmm) REVERT: A 111 HIS cc_start: 0.2834 (OUTLIER) cc_final: 0.2343 (t70) REVERT: A 186 MET cc_start: 0.5345 (mtm) cc_final: 0.4728 (mtt) REVERT: A 238 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.5971 (t80) REVERT: A 410 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: A 426 PHE cc_start: 0.3146 (OUTLIER) cc_final: 0.2831 (m-80) REVERT: A 494 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6894 (mtm180) REVERT: A 668 MET cc_start: 0.3750 (OUTLIER) cc_final: 0.3301 (ptt) REVERT: A 672 ARG cc_start: 0.3891 (OUTLIER) cc_final: 0.2558 (tpp80) REVERT: A 701 PHE cc_start: 0.7214 (m-10) cc_final: 0.6939 (m-80) REVERT: A 1144 MET cc_start: 0.4474 (tpp) cc_final: 0.3745 (ttm) REVERT: A 1185 PHE cc_start: 0.6346 (t80) cc_final: 0.5756 (t80) REVERT: A 1193 PHE cc_start: 0.7514 (t80) cc_final: 0.7224 (t80) REVERT: A 1225 TYR cc_start: 0.8056 (t80) cc_final: 0.7705 (t80) REVERT: A 1605 MET cc_start: 0.4088 (tmm) cc_final: 0.3470 (mmm) REVERT: A 1737 LYS cc_start: 0.6337 (tttp) cc_final: 0.5535 (pmtt) REVERT: B 179 PHE cc_start: 0.3396 (t80) cc_final: 0.2552 (m-80) REVERT: B 204 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5163 (tmm) REVERT: B 218 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.5644 (mtmp) REVERT: C 97 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: D 110 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: D 125 GLN cc_start: 0.7775 (mp10) cc_final: 0.7511 (mp10) REVERT: D 157 ASN cc_start: 0.7966 (m-40) cc_final: 0.7677 (m110) REVERT: D 290 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7444 (p) REVERT: D 452 GLN cc_start: 0.8174 (tt0) cc_final: 0.7877 (mt0) REVERT: D 455 GLU cc_start: 0.8401 (tp30) cc_final: 0.7682 (tp30) REVERT: D 473 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: D 528 LYS cc_start: 0.7144 (mtmm) cc_final: 0.6808 (ttmm) REVERT: D 532 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7132 (mmm160) REVERT: D 533 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7043 (pp) REVERT: E 122 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6660 (mtm180) REVERT: E 142 LYS cc_start: 0.7797 (ttpp) cc_final: 0.7446 (ttpt) REVERT: E 144 GLU cc_start: 0.7363 (tp30) cc_final: 0.7111 (tt0) REVERT: E 227 LYS cc_start: 0.8072 (ttpp) cc_final: 0.7632 (ttpp) REVERT: E 419 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: E 443 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6681 (mtm110) REVERT: F 247 LYS cc_start: 0.4946 (mttp) cc_final: 0.4518 (ttpp) outliers start: 77 outliers final: 41 residues processed: 256 average time/residue: 1.3550 time to fit residues: 385.2216 Evaluate side-chains 254 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 1.989 ------------------------------------------------------------------------------- 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 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 189 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 426 PHE 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 526 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 672 ARG 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 1700 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 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 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 110 GLU Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 450 VAL 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 532 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 127 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 0.3980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2045 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 : 0.599 10.917 23285 Z= 0.312 Chirality : 0.044 0.215 2368 Planarity : 0.006 0.135 2952 Dihedral : 4.748 32.044 2185 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 3.81 % Allowed : 22.75 % Favored : 73.45 % 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: 0.24 (0.20), residues: 1940 helix: 1.29 (0.17), residues: 994 sheet: 1.03 (0.55), residues: 89 loop : -1.33 (0.22), residues: 857 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 0.026 0.001 TYR F 226 ARG 0.016 0.001 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 271 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7850 (mm) cc_final: 0.7426 (tp) REVERT: A 47 ARG cc_start: 0.6334 (ttt90) cc_final: 0.5214 (ttp-170) REVERT: A 75 MET cc_start: 0.8355 (tpt) cc_final: 0.7936 (mmm) REVERT: A 111 HIS cc_start: 0.3052 (OUTLIER) cc_final: 0.2435 (t70) REVERT: A 186 MET cc_start: 0.5334 (mtm) cc_final: 0.4738 (mtt) REVERT: A 410 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: A 426 PHE cc_start: 0.3323 (OUTLIER) cc_final: 0.3016 (m-80) REVERT: A 494 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6952 (mtm180) REVERT: A 622 ASN cc_start: 0.1605 (OUTLIER) cc_final: 0.0167 (m-40) REVERT: A 668 MET cc_start: 0.3819 (OUTLIER) cc_final: 0.3367 (ptt) REVERT: A 672 ARG cc_start: 0.3811 (OUTLIER) cc_final: 0.2309 (ppp80) REVERT: A 701 PHE cc_start: 0.7237 (m-10) cc_final: 0.6974 (m-80) REVERT: A 1144 MET cc_start: 0.4477 (tpp) cc_final: 0.3696 (ttm) REVERT: A 1185 PHE cc_start: 0.6323 (t80) cc_final: 0.5771 (t80) REVERT: A 1193 PHE cc_start: 0.7356 (t80) cc_final: 0.7058 (t80) REVERT: A 1225 TYR cc_start: 0.8017 (t80) cc_final: 0.7688 (t80) REVERT: A 1281 SER cc_start: 0.5151 (OUTLIER) cc_final: 0.4158 (m) REVERT: A 1605 MET cc_start: 0.4105 (tmm) cc_final: 0.3519 (mmm) REVERT: A 1737 LYS cc_start: 0.6331 (tttp) cc_final: 0.5536 (pmtt) REVERT: B 179 PHE cc_start: 0.3367 (t80) cc_final: 0.2537 (m-80) REVERT: B 195 PHE cc_start: 0.4026 (t80) cc_final: 0.3808 (t80) REVERT: B 204 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5133 (tmm) REVERT: B 218 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5629 (mtmp) REVERT: B 229 PHE cc_start: 0.7604 (t80) cc_final: 0.7260 (t80) REVERT: C 97 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6441 (m-80) REVERT: D 125 GLN cc_start: 0.7700 (mp10) cc_final: 0.7438 (mp10) REVERT: D 388 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7909 (mm-30) REVERT: D 452 GLN cc_start: 0.8156 (tt0) cc_final: 0.7856 (mt0) REVERT: D 455 GLU cc_start: 0.8399 (tp30) cc_final: 0.7663 (tp30) REVERT: D 528 LYS cc_start: 0.7108 (mtmm) cc_final: 0.6779 (ttmm) REVERT: D 533 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6965 (pp) REVERT: E 97 ASP cc_start: 0.4087 (OUTLIER) cc_final: 0.3811 (p0) REVERT: E 142 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7376 (ttpt) REVERT: E 144 GLU cc_start: 0.7346 (tp30) cc_final: 0.7093 (tt0) REVERT: E 227 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7633 (ttpp) REVERT: E 419 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: E 443 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6661 (mtm110) REVERT: F 220 MET cc_start: 0.1473 (mtm) cc_final: 0.0973 (mmm) REVERT: F 247 LYS cc_start: 0.5034 (mttp) cc_final: 0.4509 (ttpp) outliers start: 68 outliers final: 36 residues processed: 252 average time/residue: 1.3654 time to fit residues: 384.1146 Evaluate side-chains 250 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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 161 MET Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 222 ASN 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 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 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 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 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 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 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 97 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 127 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 0.4980 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 0.0670 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 0.0370 chunk 54 optimal weight: 0.3980 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS E 69 GLN E 416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2063 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= 0.162 Angle : 0.574 11.098 23285 Z= 0.298 Chirality : 0.042 0.221 2368 Planarity : 0.006 0.108 2952 Dihedral : 4.598 31.315 2185 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.30 % Rotamer: Outliers : 3.03 % Allowed : 23.75 % Favored : 73.22 % 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: 0.37 (0.20), residues: 1940 helix: 1.42 (0.17), residues: 993 sheet: 1.05 (0.55), residues: 89 loop : -1.28 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 123 HIS 0.016 0.001 HIS C 17 PHE 0.029 0.001 PHE F 216 TYR 0.017 0.001 TYR F 177 ARG 0.013 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 258 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7872 (mm) cc_final: 0.7438 (tp) REVERT: A 47 ARG cc_start: 0.6269 (ttt90) cc_final: 0.5137 (ttp-170) REVERT: A 75 MET cc_start: 0.8319 (tpt) cc_final: 0.7866 (mmm) REVERT: A 111 HIS cc_start: 0.2872 (OUTLIER) cc_final: 0.2228 (t70) REVERT: A 186 MET cc_start: 0.5377 (mtm) cc_final: 0.4756 (mtt) REVERT: A 410 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 426 PHE cc_start: 0.3351 (OUTLIER) cc_final: 0.3035 (m-80) REVERT: A 494 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6507 (mtm180) REVERT: A 668 MET cc_start: 0.3819 (OUTLIER) cc_final: 0.3370 (ptt) REVERT: A 672 ARG cc_start: 0.3606 (OUTLIER) cc_final: 0.2582 (ppp80) REVERT: A 701 PHE cc_start: 0.7241 (m-10) cc_final: 0.6968 (m-80) REVERT: A 1144 MET cc_start: 0.4460 (tpp) cc_final: 0.3836 (ttm) REVERT: A 1185 PHE cc_start: 0.6328 (t80) cc_final: 0.5673 (t80) REVERT: A 1193 PHE cc_start: 0.7347 (t80) cc_final: 0.7053 (t80) REVERT: A 1225 TYR cc_start: 0.8040 (t80) cc_final: 0.7710 (t80) REVERT: A 1605 MET cc_start: 0.4014 (tmm) cc_final: 0.3479 (mmm) REVERT: A 1737 LYS cc_start: 0.6345 (tttp) cc_final: 0.5561 (pmtt) REVERT: B 179 PHE cc_start: 0.3393 (t80) cc_final: 0.2583 (m-80) REVERT: B 191 GLU cc_start: 0.2923 (OUTLIER) cc_final: 0.2073 (pt0) REVERT: B 195 PHE cc_start: 0.3979 (t80) cc_final: 0.3769 (t80) REVERT: B 204 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5098 (tmm) REVERT: B 218 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5609 (mtmp) REVERT: B 229 PHE cc_start: 0.7635 (t80) cc_final: 0.7251 (t80) REVERT: C 97 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: D 125 GLN cc_start: 0.7693 (mp10) cc_final: 0.7435 (mp10) REVERT: D 388 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7951 (mm-30) REVERT: D 452 GLN cc_start: 0.8154 (tt0) cc_final: 0.7800 (mt0) REVERT: D 455 GLU cc_start: 0.8398 (tp30) cc_final: 0.7671 (tp30) REVERT: D 533 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6894 (pp) REVERT: E 122 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6935 (mtm110) REVERT: E 142 LYS cc_start: 0.7695 (ttpp) cc_final: 0.7352 (ttpt) REVERT: E 144 GLU cc_start: 0.7349 (tp30) cc_final: 0.7106 (tt0) REVERT: E 227 LYS cc_start: 0.8009 (ttpp) cc_final: 0.7536 (ttpp) REVERT: E 419 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5601 (m-80) REVERT: E 443 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6640 (mtm110) REVERT: F 220 MET cc_start: 0.1101 (mtm) cc_final: 0.0706 (mmm) REVERT: F 247 LYS cc_start: 0.4916 (mttp) cc_final: 0.4620 (ttpp) outliers start: 54 outliers final: 29 residues processed: 240 average time/residue: 1.3681 time to fit residues: 365.3296 Evaluate side-chains 238 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 129 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 222 ASN 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 464 ILE Chi-restraints excluded: chain A residue 469 THR 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 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 1700 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 138 GLU 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 269 ILE 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 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 127 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 ASN C 17 HIS C 51 ASN E 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17193 Z= 0.215 Angle : 0.610 9.898 23285 Z= 0.317 Chirality : 0.044 0.217 2368 Planarity : 0.006 0.138 2952 Dihedral : 4.734 31.303 2185 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.40 % Rotamer: Outliers : 3.14 % Allowed : 24.15 % Favored : 72.72 % 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: 0.34 (0.20), residues: 1940 helix: 1.39 (0.17), residues: 988 sheet: 1.00 (0.55), residues: 90 loop : -1.28 (0.22), residues: 862 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 0.002 PHE F 216 TYR 0.017 0.001 TYR A 160 ARG 0.016 0.001 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 252 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 2.053 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7860 (mm) cc_final: 0.7439 (tp) REVERT: A 47 ARG cc_start: 0.6377 (ttt90) cc_final: 0.5196 (ttp-170) REVERT: A 51 MET cc_start: 0.4605 (mmp) cc_final: 0.3609 (ptm) REVERT: A 75 MET cc_start: 0.8358 (tpt) cc_final: 0.7943 (mmm) REVERT: A 111 HIS cc_start: 0.3013 (OUTLIER) cc_final: 0.2381 (t70) REVERT: A 186 MET cc_start: 0.5348 (mtm) cc_final: 0.4749 (mtt) REVERT: A 410 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: A 426 PHE cc_start: 0.3248 (OUTLIER) cc_final: 0.2961 (m-80) REVERT: A 494 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6858 (mtm180) REVERT: A 622 ASN cc_start: 0.1028 (OUTLIER) cc_final: -0.0232 (m-40) REVERT: A 668 MET cc_start: 0.3842 (OUTLIER) cc_final: 0.2890 (ptm) REVERT: A 672 ARG cc_start: 0.3658 (OUTLIER) cc_final: 0.2226 (ppp80) REVERT: A 701 PHE cc_start: 0.7270 (m-10) cc_final: 0.6989 (m-80) REVERT: A 1144 MET cc_start: 0.4399 (tpp) cc_final: 0.3848 (ttm) REVERT: A 1185 PHE cc_start: 0.6343 (t80) cc_final: 0.5778 (t80) REVERT: A 1193 PHE cc_start: 0.7352 (t80) cc_final: 0.7058 (t80) REVERT: A 1225 TYR cc_start: 0.8024 (t80) cc_final: 0.7703 (t80) REVERT: A 1281 SER cc_start: 0.5413 (OUTLIER) cc_final: 0.4460 (m) REVERT: A 1605 MET cc_start: 0.3948 (tmm) cc_final: 0.3500 (mmm) REVERT: A 1737 LYS cc_start: 0.6335 (tttp) cc_final: 0.5544 (pmtt) REVERT: B 179 PHE cc_start: 0.3409 (t80) cc_final: 0.2582 (m-80) REVERT: B 191 GLU cc_start: 0.2943 (OUTLIER) cc_final: 0.2114 (pt0) REVERT: B 204 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.5105 (tmm) REVERT: B 218 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5614 (mtmp) REVERT: B 229 PHE cc_start: 0.7595 (t80) cc_final: 0.7242 (t80) REVERT: C 97 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: D 125 GLN cc_start: 0.7700 (mp10) cc_final: 0.7432 (mp10) REVERT: D 388 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7901 (mm-30) REVERT: D 452 GLN cc_start: 0.8186 (tt0) cc_final: 0.7877 (mt0) REVERT: D 455 GLU cc_start: 0.8402 (tp30) cc_final: 0.7669 (tp30) REVERT: D 473 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: D 533 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6950 (pp) REVERT: E 142 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7372 (ttpt) REVERT: E 144 GLU cc_start: 0.7394 (tp30) cc_final: 0.7138 (tt0) REVERT: E 227 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7631 (ttpp) REVERT: E 419 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.5907 (m-80) REVERT: E 443 ARG cc_start: 0.7047 (mtm-85) cc_final: 0.6681 (mtm110) REVERT: F 220 MET cc_start: 0.1109 (mtm) cc_final: 0.0715 (mmm) REVERT: F 247 LYS cc_start: 0.4956 (mttp) cc_final: 0.4519 (ttpp) outliers start: 56 outliers final: 34 residues processed: 238 average time/residue: 1.3781 time to fit residues: 364.7249 Evaluate side-chains 244 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE 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 222 ASN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 426 PHE 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 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 1447 ASN Chi-restraints excluded: chain A residue 1450 ILE 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 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 269 ILE 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 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 81 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 193 MET 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 181 ILE 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 123 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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** A1447 ASN C 17 HIS E 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.191143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137078 restraints weight = 20597.343| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.11 r_work: 0.3776 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 17193 Z= 0.225 Angle : 0.784 59.193 23285 Z= 0.443 Chirality : 0.046 0.753 2368 Planarity : 0.006 0.138 2952 Dihedral : 4.799 40.086 2185 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 2.91 % Allowed : 24.26 % Favored : 72.83 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.05 % 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: 0.33 (0.20), residues: 1940 helix: 1.39 (0.17), residues: 988 sheet: 0.99 (0.55), residues: 90 loop : -1.30 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 123 HIS 0.005 0.001 HIS C 63 PHE 0.029 0.002 PHE F 216 TYR 0.016 0.001 TYR A 160 ARG 0.015 0.000 ARG A1761 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6717.68 seconds wall clock time: 121 minutes 8.08 seconds (7268.08 seconds total)