Starting phenix.real_space_refine on Fri Sep 11 19:35:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1n_8958/09_2026/6e1n_8958_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1n_8958/09_2026/6e1n_8958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e1n_8958/09_2026/6e1n_8958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1n_8958/09_2026/6e1n_8958.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1n_8958/09_2026/6e1n_8958_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1n_8958/09_2026/6e1n_8958_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 8 5.49 5 S 46 5.16 5 C 7164 2.51 5 N 1576 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TPO:plan-1': 2, 'PHE:plan': 1, 'GLN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TPO:plan-1': 2, 'PHE:plan': 1, 'GLN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.21 Number of scatterers: 10682 At special positions: 0 Unit cell: (137.363, 91.17, 106.973, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 46 16.00 P 8 15.00 O 1882 8.00 N 1576 7.00 C 7164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 306.4 milliseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.624A pdb=" N PHE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.626A pdb=" N PHE A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.839A pdb=" N PHE A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.533A pdb=" N TRP A 92 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 136 removed outlier: 3.830A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 150 through 173 removed outlier: 3.512A pdb=" N VAL A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 163 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 4.067A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.923A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 238 removed outlier: 4.161A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.911A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.967A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.663A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.625A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 3.630A pdb=" N LEU A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.896A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 removed outlier: 5.370A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 4.172A pdb=" N ASP A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.690A pdb=" N LEU A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.622A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.977A pdb=" N THR A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 487 removed outlier: 3.723A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 Processing helix chain 'A' and resid 496 through 513 removed outlier: 3.616A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 534 through 539 removed outlier: 4.281A pdb=" N MET A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 551 through 565 removed outlier: 3.696A pdb=" N ILE A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 567 through 587 removed outlier: 4.028A pdb=" N ILE A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.668A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.812A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.960A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 688 removed outlier: 3.545A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.564A pdb=" N PHE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.719A pdb=" N PHE B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 78 through 87 removed outlier: 4.705A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.534A pdb=" N TRP B 92 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 136 removed outlier: 3.823A pdb=" N ILE B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 150 through 173 removed outlier: 3.959A pdb=" N LYS B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 4.044A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 193 " --> pdb=" O TYR B 189 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.927A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 238 removed outlier: 4.205A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.901A pdb=" N LEU B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.981A pdb=" N GLN B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.666A pdb=" N VAL B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.567A pdb=" N LEU B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 333 removed outlier: 3.654A pdb=" N LEU B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 355 removed outlier: 4.060A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 removed outlier: 5.159A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 4.151A pdb=" N LEU B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.714A pdb=" N LEU B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 456 removed outlier: 3.909A pdb=" N THR B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 487 removed outlier: 3.751A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 477 " --> pdb=" O TRP B 473 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 493 Processing helix chain 'B' and resid 496 through 513 removed outlier: 3.692A pdb=" N LEU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 534 through 539 removed outlier: 4.223A pdb=" N MET B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.616A pdb=" N ILE B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 567 through 587 removed outlier: 4.095A pdb=" N ILE B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 616 through 629 removed outlier: 3.644A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.778A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 663 removed outlier: 3.974A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 688 removed outlier: 3.557A pdb=" N LEU B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1470 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: 1.61 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1657 1.31 - 1.43: 3084 1.43 - 1.56: 6077 1.56 - 1.68: 32 1.68 - 1.81: 74 Bond restraints: 10924 Sorted by residual: bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C31 3PH A 812 " pdb=" O31 3PH A 812 " ideal model delta sigma weight residual 1.325 1.409 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 13485 2.49 - 4.98: 1060 4.98 - 7.46: 147 7.46 - 9.95: 61 9.95 - 12.44: 11 Bond angle restraints: 14764 Sorted by residual: angle pdb=" C ILE A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta sigma weight residual 121.19 130.14 -8.95 1.59e+00 3.96e-01 3.17e+01 angle pdb=" C ILE B 371 " pdb=" N PHE B 372 " pdb=" CA PHE B 372 " ideal model delta sigma weight residual 121.19 130.12 -8.93 1.59e+00 3.96e-01 3.15e+01 angle pdb=" C THR B 264 " pdb=" CA THR B 264 " pdb=" CB THR B 264 " ideal model delta sigma weight residual 111.80 104.25 7.55 1.46e+00 4.69e-01 2.67e+01 angle pdb=" C THR A 264 " pdb=" CA THR A 264 " pdb=" CB THR A 264 " ideal model delta sigma weight residual 111.80 104.38 7.42 1.46e+00 4.69e-01 2.58e+01 angle pdb=" C VAL A 628 " pdb=" N MET A 629 " pdb=" CA MET A 629 " ideal model delta sigma weight residual 122.35 129.25 -6.90 1.46e+00 4.69e-01 2.23e+01 ... (remaining 14759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5731 17.40 - 34.80: 478 34.80 - 52.20: 113 52.20 - 69.61: 38 69.61 - 87.01: 6 Dihedral angle restraints: 6366 sinusoidal: 2590 harmonic: 3776 Sorted by residual: dihedral pdb=" CA THR B 378 " pdb=" C THR B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual -180.00 -133.46 -46.54 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LEU B 661 " pdb=" CA LEU B 661 " ideal model delta harmonic sigma weight residual 180.00 135.77 44.23 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LEU A 661 " pdb=" CA LEU A 661 " ideal model delta harmonic sigma weight residual 180.00 138.04 41.96 0 5.00e+00 4.00e-02 7.04e+01 ... (remaining 6363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1276 0.081 - 0.163: 322 0.163 - 0.244: 46 0.244 - 0.325: 2 0.325 - 0.407: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C2 3PH A 812 " pdb=" C1 3PH A 812 " pdb=" C3 3PH A 812 " pdb=" O21 3PH A 812 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1647 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 587 " -0.035 2.00e-02 2.50e+03 2.34e-02 9.55e+00 pdb=" CG PHE B 587 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 587 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 587 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 587 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 153 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" CG ASN A 153 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 153 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 153 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 89 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO A 90 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.040 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 174 2.62 - 3.19: 9880 3.19 - 3.76: 16307 3.76 - 4.33: 22979 4.33 - 4.90: 35682 Nonbonded interactions: 85022 Sorted by model distance: nonbonded pdb=" O LEU B 197 " pdb=" NH1 ARG B 203 " model vdw 2.054 3.120 nonbonded pdb=" O LEU A 197 " pdb=" NH1 ARG A 203 " model vdw 2.058 3.120 nonbonded pdb=" OD2 ASP A 606 " pdb=" O HOH A 901 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS B 344 " pdb=" OG SER B 364 " model vdw 2.209 3.120 nonbonded pdb=" OD2 ASP B 606 " pdb=" O HOH B 901 " model vdw 2.236 3.040 ... (remaining 85017 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 0.015 0.124 10942 Z= 0.654 Angle : 1.548 12.441 14764 Z= 0.818 Chirality : 0.072 0.407 1650 Planarity : 0.008 0.071 1794 Dihedral : 14.721 87.007 3926 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.25 % Favored : 91.59 % Rotamer: Outliers : 0.37 % Allowed : 2.89 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.21 (0.17), residues: 1248 helix: -3.82 (0.11), residues: 732 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 537 TYR 0.034 0.005 TYR B 532 PHE 0.047 0.005 PHE B 587 TRP 0.030 0.005 TRP A 529 HIS 0.004 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.01500 / 0.65 (10924) covalent geometry : angle 1.54760 / 0.82 (14764) hydrogen bonds : bond 0.31387 / 20.28 ( 503) hydrogen bonds : angle 10.60269 / 7.28 ( 1470) Misc. bond : bond 0.00363 / 0.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 409 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8775 (m-30) cc_final: 0.8317 (m-30) REVERT: A 77 ASN cc_start: 0.8438 (m-40) cc_final: 0.8235 (t0) REVERT: A 95 LYS cc_start: 0.8537 (tttt) cc_final: 0.8118 (tppt) REVERT: A 96 ASN cc_start: 0.8646 (p0) cc_final: 0.8039 (p0) REVERT: A 121 ILE cc_start: 0.9204 (mm) cc_final: 0.8961 (mm) REVERT: A 141 TYR cc_start: 0.8677 (p90) cc_final: 0.8376 (p90) REVERT: A 194 ILE cc_start: 0.8466 (mt) cc_final: 0.8186 (mt) REVERT: A 200 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7792 (ttt90) REVERT: A 210 SER cc_start: 0.8986 (m) cc_final: 0.8595 (p) REVERT: A 220 LEU cc_start: 0.9117 (tp) cc_final: 0.8604 (tt) REVERT: A 238 PHE cc_start: 0.8849 (m-10) cc_final: 0.8628 (m-10) REVERT: A 321 GLN cc_start: 0.8394 (mt0) cc_final: 0.8114 (pp30) REVERT: A 326 MET cc_start: 0.8644 (mmm) cc_final: 0.8439 (tpt) REVERT: A 438 PHE cc_start: 0.7520 (m-80) cc_final: 0.7276 (m-80) REVERT: A 491 TYR cc_start: 0.7374 (t80) cc_final: 0.7067 (t80) REVERT: A 499 PHE cc_start: 0.8788 (m-10) cc_final: 0.8543 (m-80) REVERT: A 602 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7644 (mm-30) REVERT: A 637 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7153 (tm-30) REVERT: A 683 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7746 (tt0) REVERT: A 687 CYS cc_start: 0.5548 (m) cc_final: 0.4869 (t) REVERT: B 95 LYS cc_start: 0.8550 (tttt) cc_final: 0.8111 (tppt) REVERT: B 96 ASN cc_start: 0.8664 (p0) cc_final: 0.8115 (p0) REVERT: B 121 ILE cc_start: 0.9194 (mm) cc_final: 0.8964 (mm) REVERT: B 141 TYR cc_start: 0.8665 (p90) cc_final: 0.8352 (p90) REVERT: B 152 LEU cc_start: 0.8053 (tp) cc_final: 0.7799 (tt) REVERT: B 166 ASP cc_start: 0.8479 (t0) cc_final: 0.7837 (t70) REVERT: B 194 ILE cc_start: 0.8474 (mt) cc_final: 0.8176 (mt) REVERT: B 200 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7786 (ttt90) REVERT: B 210 SER cc_start: 0.8966 (m) cc_final: 0.8607 (p) REVERT: B 220 LEU cc_start: 0.9105 (tp) cc_final: 0.8392 (tt) REVERT: B 497 ASN cc_start: 0.8190 (t0) cc_final: 0.7926 (t0) REVERT: B 499 PHE cc_start: 0.8828 (m-10) cc_final: 0.8552 (m-80) REVERT: B 544 LEU cc_start: 0.7830 (mt) cc_final: 0.7470 (tp) REVERT: B 602 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7626 (mm-30) REVERT: B 606 ASP cc_start: 0.9083 (m-30) cc_final: 0.8403 (m-30) REVERT: B 637 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7156 (tm-30) REVERT: B 683 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7760 (mt-10) outliers start: 4 outliers final: 1 residues processed: 413 average time/residue: 0.0862 time to fit residues: 51.8927 Evaluate side-chains 302 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 613 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 89 GLN A 257 GLN A 454 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 89 GLN B 257 GLN B 454 ASN B 612 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.203375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.160220 restraints weight = 16363.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164369 restraints weight = 7561.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166899 restraints weight = 4652.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.168306 restraints weight = 3528.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.168888 restraints weight = 3051.293| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10942 Z= 0.179 Angle : 0.795 9.731 14764 Z= 0.410 Chirality : 0.045 0.216 1650 Planarity : 0.005 0.037 1794 Dihedral : 14.533 77.675 1686 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.61 % Allowed : 11.64 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.20), residues: 1248 helix: -2.38 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -2.05 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.019 0.002 TYR B 114 PHE 0.020 0.002 PHE B 624 TRP 0.014 0.002 TRP B 271 HIS 0.001 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (10924) covalent geometry : angle 0.79510 / 0.41 (14764) hydrogen bonds : bond 0.05716 / 3.69 ( 503) hydrogen bonds : angle 5.81346 / 4.08 ( 1470) Misc. bond : bond 0.00178 / 0.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 346 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8274 (tttt) cc_final: 0.7979 (tttt) REVERT: A 96 ASN cc_start: 0.8036 (p0) cc_final: 0.7329 (p0) REVERT: A 121 ILE cc_start: 0.8679 (mm) cc_final: 0.8368 (mm) REVERT: A 166 ASP cc_start: 0.7961 (t70) cc_final: 0.6761 (t0) REVERT: A 210 SER cc_start: 0.8797 (m) cc_final: 0.8572 (t) REVERT: A 326 MET cc_start: 0.8449 (mmm) cc_final: 0.8155 (tpt) REVERT: A 372 PHE cc_start: 0.7457 (m-10) cc_final: 0.7033 (t80) REVERT: A 398 ARG cc_start: 0.6681 (mtm-85) cc_final: 0.6385 (mtp180) REVERT: A 542 ILE cc_start: 0.7605 (pt) cc_final: 0.7131 (pt) REVERT: A 544 LEU cc_start: 0.8402 (mt) cc_final: 0.8026 (tp) REVERT: A 637 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7337 (tm-30) REVERT: A 683 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7649 (mt-10) REVERT: B 81 LEU cc_start: 0.9108 (tp) cc_final: 0.8615 (tt) REVERT: B 95 LYS cc_start: 0.8287 (tttt) cc_final: 0.8051 (tttt) REVERT: B 96 ASN cc_start: 0.8065 (p0) cc_final: 0.7430 (p0) REVERT: B 121 ILE cc_start: 0.8719 (mm) cc_final: 0.8411 (mm) REVERT: B 141 TYR cc_start: 0.8647 (p90) cc_final: 0.8419 (p90) REVERT: B 152 LEU cc_start: 0.8123 (tp) cc_final: 0.7902 (mt) REVERT: B 354 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8039 (tp) REVERT: B 438 PHE cc_start: 0.7523 (m-80) cc_final: 0.7209 (m-80) REVERT: B 544 LEU cc_start: 0.7599 (mt) cc_final: 0.7239 (tp) REVERT: B 637 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7312 (tm-30) REVERT: B 684 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6633 (mm-30) outliers start: 28 outliers final: 12 residues processed: 358 average time/residue: 0.0813 time to fit residues: 42.8639 Evaluate side-chains 298 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 285 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 134 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 134 HIS B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.201207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.157128 restraints weight = 16441.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161131 restraints weight = 7766.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163565 restraints weight = 4866.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164962 restraints weight = 3714.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.165451 restraints weight = 3224.001| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10942 Z= 0.203 Angle : 0.744 8.601 14764 Z= 0.382 Chirality : 0.045 0.189 1650 Planarity : 0.004 0.036 1794 Dihedral : 13.489 75.852 1686 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.17 % Allowed : 15.55 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.21), residues: 1248 helix: -1.78 (0.15), residues: 858 sheet: None (None), residues: 0 loop : -1.78 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 62 TYR 0.019 0.002 TYR A 173 PHE 0.028 0.002 PHE A 438 TRP 0.013 0.001 TRP B 271 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (10924) covalent geometry : angle 0.74369 / 0.38 (14764) hydrogen bonds : bond 0.04985 / 3.31 ( 503) hydrogen bonds : angle 5.33162 / 3.74 ( 1470) Misc. bond : bond 0.00148 / 0.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8080 (p0) cc_final: 0.7412 (p0) REVERT: A 114 TYR cc_start: 0.6795 (m-10) cc_final: 0.6423 (m-10) REVERT: A 119 GLU cc_start: 0.7346 (tp30) cc_final: 0.7071 (tm-30) REVERT: A 121 ILE cc_start: 0.8806 (mm) cc_final: 0.8496 (mm) REVERT: A 210 SER cc_start: 0.8817 (m) cc_final: 0.8612 (t) REVERT: A 326 MET cc_start: 0.8571 (mmm) cc_final: 0.8164 (tpt) REVERT: A 372 PHE cc_start: 0.7502 (m-10) cc_final: 0.7038 (t80) REVERT: A 438 PHE cc_start: 0.7368 (m-80) cc_final: 0.7083 (m-80) REVERT: A 542 ILE cc_start: 0.7603 (pt) cc_final: 0.7242 (pt) REVERT: A 544 LEU cc_start: 0.8473 (mt) cc_final: 0.8219 (tp) REVERT: A 638 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8747 (t) REVERT: A 640 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8170 (ttpt) REVERT: A 683 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7696 (mt-10) REVERT: B 96 ASN cc_start: 0.8096 (p0) cc_final: 0.7450 (p0) REVERT: B 121 ILE cc_start: 0.8830 (mm) cc_final: 0.8494 (mm) REVERT: B 141 TYR cc_start: 0.8602 (p90) cc_final: 0.8355 (p90) REVERT: B 152 LEU cc_start: 0.8146 (tp) cc_final: 0.7869 (mt) REVERT: B 438 PHE cc_start: 0.7544 (m-80) cc_final: 0.7343 (m-80) REVERT: B 615 ASP cc_start: 0.7134 (m-30) cc_final: 0.6911 (m-30) REVERT: B 637 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7423 (tm-30) outliers start: 34 outliers final: 29 residues processed: 310 average time/residue: 0.0825 time to fit residues: 37.9148 Evaluate side-chains 301 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.0030 chunk 96 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 242 GLN A 585 GLN B 89 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.203712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.160914 restraints weight = 16390.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.165076 restraints weight = 7603.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167584 restraints weight = 4666.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.168828 restraints weight = 3511.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.169711 restraints weight = 3052.261| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10942 Z= 0.149 Angle : 0.704 8.717 14764 Z= 0.355 Chirality : 0.043 0.173 1650 Planarity : 0.004 0.035 1794 Dihedral : 12.684 74.830 1686 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.79 % Allowed : 18.16 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.22), residues: 1248 helix: -1.35 (0.16), residues: 838 sheet: None (None), residues: 0 loop : -1.85 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.024 0.002 TYR A 491 PHE 0.028 0.002 PHE B 137 TRP 0.013 0.001 TRP B 271 HIS 0.007 0.002 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10924) covalent geometry : angle 0.70365 / 0.35 (14764) hydrogen bonds : bond 0.04323 / 2.86 ( 503) hydrogen bonds : angle 5.10126 / 3.57 ( 1470) Misc. bond : bond 0.00112 / 0.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 302 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9214 (tp) cc_final: 0.8844 (tt) REVERT: A 96 ASN cc_start: 0.7974 (p0) cc_final: 0.7360 (p0) REVERT: A 121 ILE cc_start: 0.8814 (mm) cc_final: 0.8493 (mm) REVERT: A 127 THR cc_start: 0.9035 (m) cc_final: 0.8824 (p) REVERT: A 194 ILE cc_start: 0.8444 (mt) cc_final: 0.8165 (mp) REVERT: A 438 PHE cc_start: 0.7284 (m-80) cc_final: 0.7055 (m-80) REVERT: A 542 ILE cc_start: 0.7772 (pt) cc_final: 0.7404 (pt) REVERT: A 578 ILE cc_start: 0.8949 (mm) cc_final: 0.8749 (mm) REVERT: A 620 MET cc_start: 0.8581 (tpp) cc_final: 0.8292 (tpp) REVERT: A 638 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8743 (t) REVERT: A 683 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 76 LEU cc_start: 0.9212 (tp) cc_final: 0.8885 (tt) REVERT: B 96 ASN cc_start: 0.7918 (p0) cc_final: 0.7332 (p0) REVERT: B 121 ILE cc_start: 0.8769 (mm) cc_final: 0.8440 (mm) REVERT: B 127 THR cc_start: 0.9040 (m) cc_final: 0.8778 (p) REVERT: B 152 LEU cc_start: 0.8169 (tp) cc_final: 0.7958 (mt) REVERT: B 166 ASP cc_start: 0.7789 (t70) cc_final: 0.7438 (t0) REVERT: B 194 ILE cc_start: 0.8431 (mt) cc_final: 0.8166 (mp) REVERT: B 438 PHE cc_start: 0.7573 (m-80) cc_final: 0.7340 (m-80) REVERT: B 554 PHE cc_start: 0.8080 (t80) cc_final: 0.7840 (t80) outliers start: 30 outliers final: 17 residues processed: 315 average time/residue: 0.0818 time to fit residues: 38.5438 Evaluate side-chains 298 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 280 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 549 GLN A 585 GLN B 89 GLN B 242 GLN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.206079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164803 restraints weight = 16259.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168931 restraints weight = 7453.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171479 restraints weight = 4496.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.172877 restraints weight = 3341.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.173434 restraints weight = 2860.781| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.136 Angle : 0.675 8.759 14764 Z= 0.339 Chirality : 0.042 0.145 1650 Planarity : 0.003 0.033 1794 Dihedral : 12.154 73.949 1686 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.61 % Allowed : 20.58 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.22), residues: 1248 helix: -0.99 (0.16), residues: 832 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.020 0.002 TYR A 491 PHE 0.022 0.001 PHE A 399 TRP 0.011 0.001 TRP B 271 HIS 0.006 0.002 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10924) covalent geometry : angle 0.67532 / 0.34 (14764) hydrogen bonds : bond 0.03999 / 2.66 ( 503) hydrogen bonds : angle 4.87348 / 3.41 ( 1470) Misc. bond : bond 0.00119 / 0.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9172 (tp) cc_final: 0.8796 (tt) REVERT: A 96 ASN cc_start: 0.7698 (p0) cc_final: 0.7172 (p0) REVERT: A 121 ILE cc_start: 0.8766 (mm) cc_final: 0.8384 (mm) REVERT: A 194 ILE cc_start: 0.8478 (mt) cc_final: 0.8224 (mp) REVERT: A 288 TYR cc_start: 0.8985 (t80) cc_final: 0.8735 (t80) REVERT: A 326 MET cc_start: 0.8356 (tpt) cc_final: 0.8095 (tpt) REVERT: A 683 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7446 (mt-10) REVERT: B 76 LEU cc_start: 0.9150 (tp) cc_final: 0.8809 (tt) REVERT: B 96 ASN cc_start: 0.7799 (p0) cc_final: 0.7230 (p0) REVERT: B 121 ILE cc_start: 0.8704 (mm) cc_final: 0.8374 (mm) REVERT: B 152 LEU cc_start: 0.8162 (tp) cc_final: 0.7949 (mt) REVERT: B 166 ASP cc_start: 0.7772 (t70) cc_final: 0.7370 (t0) REVERT: B 194 ILE cc_start: 0.8553 (mt) cc_final: 0.8279 (mp) REVERT: B 438 PHE cc_start: 0.7589 (m-80) cc_final: 0.7364 (m-80) REVERT: B 554 PHE cc_start: 0.8082 (t80) cc_final: 0.7842 (t80) outliers start: 28 outliers final: 18 residues processed: 310 average time/residue: 0.0831 time to fit residues: 38.1159 Evaluate side-chains 295 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 277 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN B 89 GLN B 497 ASN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.207352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166326 restraints weight = 16313.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170375 restraints weight = 7418.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172787 restraints weight = 4478.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174098 restraints weight = 3352.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.174741 restraints weight = 2890.920| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10942 Z= 0.137 Angle : 0.681 9.579 14764 Z= 0.336 Chirality : 0.041 0.162 1650 Planarity : 0.003 0.031 1794 Dihedral : 11.792 73.536 1686 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.14 % Allowed : 21.97 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1248 helix: -0.72 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -1.64 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 543 TYR 0.033 0.002 TYR B 491 PHE 0.030 0.002 PHE A 438 TRP 0.013 0.001 TRP B 492 HIS 0.006 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10924) covalent geometry : angle 0.68055 / 0.34 (14764) hydrogen bonds : bond 0.03939 / 2.64 ( 503) hydrogen bonds : angle 4.88557 / 3.44 ( 1470) Misc. bond : bond 0.00112 / 0.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9145 (tp) cc_final: 0.8773 (tt) REVERT: A 96 ASN cc_start: 0.7804 (p0) cc_final: 0.7188 (p0) REVERT: A 121 ILE cc_start: 0.8600 (mm) cc_final: 0.8207 (mm) REVERT: A 194 ILE cc_start: 0.8502 (mt) cc_final: 0.8230 (mp) REVERT: A 288 TYR cc_start: 0.9029 (t80) cc_final: 0.8762 (t80) REVERT: A 438 PHE cc_start: 0.7062 (m-80) cc_final: 0.6789 (m-80) REVERT: A 544 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.7339 (mt) REVERT: A 620 MET cc_start: 0.8570 (tpp) cc_final: 0.7614 (mpp) REVERT: A 683 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 76 LEU cc_start: 0.9153 (tp) cc_final: 0.8798 (tt) REVERT: B 96 ASN cc_start: 0.7787 (p0) cc_final: 0.7239 (p0) REVERT: B 121 ILE cc_start: 0.8730 (mm) cc_final: 0.8370 (mm) REVERT: B 152 LEU cc_start: 0.8155 (tp) cc_final: 0.7949 (mt) REVERT: B 166 ASP cc_start: 0.7818 (t70) cc_final: 0.7408 (t0) REVERT: B 194 ILE cc_start: 0.8510 (mt) cc_final: 0.8218 (mp) REVERT: B 438 PHE cc_start: 0.7572 (m-80) cc_final: 0.7369 (m-80) REVERT: B 560 THR cc_start: 0.8914 (p) cc_final: 0.8690 (t) outliers start: 23 outliers final: 18 residues processed: 302 average time/residue: 0.0813 time to fit residues: 36.4121 Evaluate side-chains 297 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 278 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 0.0040 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN B 85 ASN B 134 HIS B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.208028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.167407 restraints weight = 16309.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.171541 restraints weight = 7371.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.174023 restraints weight = 4419.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.175367 restraints weight = 3288.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.175855 restraints weight = 2824.502| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10942 Z= 0.127 Angle : 0.676 9.938 14764 Z= 0.331 Chirality : 0.040 0.138 1650 Planarity : 0.003 0.031 1794 Dihedral : 11.274 73.357 1686 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.23 % Allowed : 23.09 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.23), residues: 1248 helix: -0.53 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -1.72 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.024 0.002 TYR B 141 PHE 0.023 0.001 PHE A 226 TRP 0.008 0.001 TRP B 271 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10924) covalent geometry : angle 0.67623 / 0.33 (14764) hydrogen bonds : bond 0.03719 / 2.50 ( 503) hydrogen bonds : angle 4.72764 / 3.31 ( 1470) Misc. bond : bond 0.00099 / 0.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7734 (p0) cc_final: 0.7186 (p0) REVERT: A 121 ILE cc_start: 0.8476 (mm) cc_final: 0.8129 (mm) REVERT: A 194 ILE cc_start: 0.8459 (mt) cc_final: 0.8195 (mp) REVERT: A 245 LEU cc_start: 0.8650 (tt) cc_final: 0.7626 (mm) REVERT: A 438 PHE cc_start: 0.7221 (m-80) cc_final: 0.6953 (m-80) REVERT: A 679 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8199 (tm) REVERT: A 683 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7266 (mt-10) REVERT: B 76 LEU cc_start: 0.9085 (tp) cc_final: 0.8708 (tt) REVERT: B 96 ASN cc_start: 0.7760 (p0) cc_final: 0.7201 (p0) REVERT: B 121 ILE cc_start: 0.8597 (mm) cc_final: 0.8224 (mm) REVERT: B 139 ILE cc_start: 0.8627 (mt) cc_final: 0.8369 (pt) REVERT: B 166 ASP cc_start: 0.7814 (t70) cc_final: 0.7425 (t0) REVERT: B 194 ILE cc_start: 0.8531 (mt) cc_final: 0.8304 (mp) REVERT: B 245 LEU cc_start: 0.8632 (tt) cc_final: 0.7571 (mm) REVERT: B 560 THR cc_start: 0.8919 (p) cc_final: 0.8708 (t) outliers start: 24 outliers final: 13 residues processed: 311 average time/residue: 0.0828 time to fit residues: 38.3484 Evaluate side-chains 302 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 288 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN B 27 HIS B 89 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.207663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.166343 restraints weight = 16220.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170363 restraints weight = 7534.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172739 restraints weight = 4578.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.174014 restraints weight = 3459.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.174434 restraints weight = 3000.376| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10942 Z= 0.131 Angle : 0.705 11.466 14764 Z= 0.338 Chirality : 0.041 0.139 1650 Planarity : 0.003 0.030 1794 Dihedral : 10.971 73.224 1684 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.49 % Allowed : 24.39 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.23), residues: 1248 helix: -0.40 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -1.67 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 543 TYR 0.026 0.002 TYR B 288 PHE 0.024 0.001 PHE A 226 TRP 0.007 0.001 TRP B 271 HIS 0.009 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10924) covalent geometry : angle 0.70451 / 0.34 (14764) hydrogen bonds : bond 0.03655 / 2.49 ( 503) hydrogen bonds : angle 4.67361 / 3.26 ( 1470) Misc. bond : bond 0.00092 / 0.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7730 (p0) cc_final: 0.7202 (p0) REVERT: A 121 ILE cc_start: 0.8548 (mm) cc_final: 0.8132 (mm) REVERT: A 194 ILE cc_start: 0.8499 (mt) cc_final: 0.8252 (mp) REVERT: A 206 LEU cc_start: 0.9239 (tp) cc_final: 0.8944 (mp) REVERT: A 245 LEU cc_start: 0.8615 (tt) cc_final: 0.7557 (mm) REVERT: A 312 LEU cc_start: 0.9607 (tp) cc_final: 0.9405 (tp) REVERT: A 683 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7267 (mt-10) REVERT: B 96 ASN cc_start: 0.7747 (p0) cc_final: 0.7205 (p0) REVERT: B 121 ILE cc_start: 0.8560 (mm) cc_final: 0.8180 (mm) REVERT: B 139 ILE cc_start: 0.8650 (mt) cc_final: 0.8402 (pt) REVERT: B 166 ASP cc_start: 0.7748 (t70) cc_final: 0.7314 (t0) REVERT: B 194 ILE cc_start: 0.8542 (mt) cc_final: 0.8295 (mp) REVERT: B 245 LEU cc_start: 0.8603 (tt) cc_final: 0.8106 (tt) REVERT: B 403 GLU cc_start: 0.6169 (tp30) cc_final: 0.5908 (tp30) REVERT: B 560 THR cc_start: 0.8892 (p) cc_final: 0.8691 (t) outliers start: 16 outliers final: 14 residues processed: 284 average time/residue: 0.0858 time to fit residues: 36.3437 Evaluate side-chains 277 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 491 TYR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.208880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167467 restraints weight = 16143.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.171515 restraints weight = 7419.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173908 restraints weight = 4502.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.175073 restraints weight = 3377.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.175883 restraints weight = 2949.181| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10942 Z= 0.132 Angle : 0.715 10.856 14764 Z= 0.345 Chirality : 0.041 0.187 1650 Planarity : 0.004 0.051 1794 Dihedral : 10.735 73.253 1684 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.86 % Allowed : 24.12 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.23), residues: 1248 helix: -0.19 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -1.53 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.042 0.002 TYR B 288 PHE 0.047 0.001 PHE A 438 TRP 0.007 0.001 TRP A 271 HIS 0.008 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10924) covalent geometry : angle 0.71452 / 0.34 (14764) hydrogen bonds : bond 0.03589 / 2.41 ( 503) hydrogen bonds : angle 4.69758 / 3.27 ( 1470) Misc. bond : bond 0.00090 / 0.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7798 (p0) cc_final: 0.7258 (p0) REVERT: A 121 ILE cc_start: 0.8499 (mm) cc_final: 0.8092 (mm) REVERT: A 194 ILE cc_start: 0.8547 (mt) cc_final: 0.8260 (mp) REVERT: A 206 LEU cc_start: 0.9273 (tp) cc_final: 0.8972 (mp) REVERT: A 245 LEU cc_start: 0.8571 (tt) cc_final: 0.7559 (mm) REVERT: A 312 LEU cc_start: 0.9614 (tp) cc_final: 0.9407 (tp) REVERT: A 326 MET cc_start: 0.8264 (tpt) cc_final: 0.7858 (tpt) REVERT: A 673 GLU cc_start: 0.7738 (tp30) cc_final: 0.7534 (tp30) REVERT: A 683 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7182 (mt-10) REVERT: B 81 LEU cc_start: 0.8807 (tp) cc_final: 0.8459 (tt) REVERT: B 96 ASN cc_start: 0.7799 (p0) cc_final: 0.7269 (p0) REVERT: B 121 ILE cc_start: 0.8612 (mm) cc_final: 0.8257 (mm) REVERT: B 139 ILE cc_start: 0.8634 (mt) cc_final: 0.8312 (pt) REVERT: B 166 ASP cc_start: 0.7788 (t70) cc_final: 0.7441 (t0) REVERT: B 194 ILE cc_start: 0.8539 (mt) cc_final: 0.8273 (mp) REVERT: B 212 MET cc_start: 0.8532 (mmm) cc_final: 0.7845 (mtt) REVERT: B 245 LEU cc_start: 0.8565 (tt) cc_final: 0.7564 (mm) REVERT: B 403 GLU cc_start: 0.6226 (tp30) cc_final: 0.5876 (tp30) REVERT: B 438 PHE cc_start: 0.7496 (m-80) cc_final: 0.7229 (m-80) REVERT: B 560 THR cc_start: 0.8855 (p) cc_final: 0.8647 (t) outliers start: 20 outliers final: 13 residues processed: 280 average time/residue: 0.0742 time to fit residues: 31.2393 Evaluate side-chains 282 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.207372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165729 restraints weight = 16191.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.169685 restraints weight = 7537.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.172038 restraints weight = 4646.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.173419 restraints weight = 3526.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.173925 restraints weight = 3041.923| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10942 Z= 0.139 Angle : 0.723 11.029 14764 Z= 0.347 Chirality : 0.042 0.218 1650 Planarity : 0.004 0.034 1794 Dihedral : 10.706 80.824 1684 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.58 % Allowed : 24.49 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1248 helix: -0.06 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -1.47 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 543 TYR 0.041 0.002 TYR B 288 PHE 0.028 0.001 PHE A 226 TRP 0.008 0.001 TRP A 271 HIS 0.008 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10924) covalent geometry : angle 0.72285 / 0.35 (14764) hydrogen bonds : bond 0.03547 / 2.40 ( 503) hydrogen bonds : angle 4.69730 / 3.26 ( 1470) Misc. bond : bond 0.00132 / 0.07 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7802 (p0) cc_final: 0.7265 (p0) REVERT: A 121 ILE cc_start: 0.8484 (mm) cc_final: 0.8077 (mm) REVERT: A 139 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8256 (pt) REVERT: A 194 ILE cc_start: 0.8491 (mt) cc_final: 0.8178 (mp) REVERT: A 206 LEU cc_start: 0.9269 (tp) cc_final: 0.8967 (mp) REVERT: A 245 LEU cc_start: 0.8531 (tt) cc_final: 0.7527 (mm) REVERT: A 312 LEU cc_start: 0.9616 (tp) cc_final: 0.9402 (tp) REVERT: A 326 MET cc_start: 0.8219 (tpt) cc_final: 0.7790 (tpt) REVERT: A 683 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7174 (mt-10) REVERT: B 81 LEU cc_start: 0.8825 (tp) cc_final: 0.8513 (tt) REVERT: B 96 ASN cc_start: 0.7795 (p0) cc_final: 0.7275 (p0) REVERT: B 139 ILE cc_start: 0.8643 (mt) cc_final: 0.8319 (pt) REVERT: B 166 ASP cc_start: 0.7815 (t70) cc_final: 0.7346 (t0) REVERT: B 194 ILE cc_start: 0.8563 (mt) cc_final: 0.8302 (mp) REVERT: B 212 MET cc_start: 0.8439 (mmm) cc_final: 0.7884 (mtt) REVERT: B 403 GLU cc_start: 0.6224 (tp30) cc_final: 0.5870 (tp30) REVERT: B 438 PHE cc_start: 0.7599 (m-80) cc_final: 0.7283 (m-80) outliers start: 17 outliers final: 16 residues processed: 279 average time/residue: 0.0805 time to fit residues: 34.0839 Evaluate side-chains 285 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 268 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 585 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.207449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166597 restraints weight = 16261.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.170576 restraints weight = 7519.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.172922 restraints weight = 4579.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.174225 restraints weight = 3458.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.174882 restraints weight = 2984.722| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10942 Z= 0.138 Angle : 0.710 10.750 14764 Z= 0.342 Chirality : 0.041 0.162 1650 Planarity : 0.004 0.033 1794 Dihedral : 10.585 81.259 1684 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.49 % Allowed : 25.33 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.23), residues: 1248 helix: 0.03 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -1.52 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.041 0.002 TYR B 288 PHE 0.028 0.001 PHE A 226 TRP 0.009 0.001 TRP A 271 HIS 0.008 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10924) covalent geometry : angle 0.70978 / 0.34 (14764) hydrogen bonds : bond 0.03490 / 2.36 ( 503) hydrogen bonds : angle 4.66267 / 3.23 ( 1470) Misc. bond : bond 0.00105 / 0.05 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1880.81 seconds wall clock time: 33 minutes 8.27 seconds (1988.27 seconds total)