Starting phenix.real_space_refine on Fri Jul 3 16:25:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pvh_71891/07_2026/9pvh_71891.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pvh_71891/07_2026/9pvh_71891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pvh_71891/07_2026/9pvh_71891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pvh_71891/07_2026/9pvh_71891.map" model { file = "/net/cci-nas-00/data/ceres_data/9pvh_71891/07_2026/9pvh_71891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pvh_71891/07_2026/9pvh_71891.cif" } resolution = 4.38 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= 0.008 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9253 2.51 5 N 2550 2.21 5 O 2693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14580 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5632 Classifications: {'peptide': 691} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 674} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 8948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 8948 Classifications: {'peptide': 1171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 68, 'TRANS': 1102} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 2.76, per 1000 atoms: 0.19 Number of scatterers: 14580 At special positions: 0 Unit cell: (105.78, 114.38, 161.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2693 8.00 N 2550 7.00 C 9253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 651.2 milliseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 2 sheets defined 79.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.683A pdb=" N TYR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.601A pdb=" N LYS A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N HIS A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 153 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.725A pdb=" N ASP A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 removed outlier: 3.980A pdb=" N MET A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.713A pdb=" N SER A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.646A pdb=" N PHE A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.157A pdb=" N GLU A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 278 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.877A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.866A pdb=" N LEU A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N HIS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.688A pdb=" N LEU A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 349 removed outlier: 3.765A pdb=" N LYS A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.828A pdb=" N LYS A 359 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 378 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.591A pdb=" N VAL A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 removed outlier: 3.956A pdb=" N GLU A 407 " --> pdb=" O ASN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.663A pdb=" N ARG A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 468 through 483 removed outlier: 3.709A pdb=" N GLU A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 4.569A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 515 removed outlier: 4.039A pdb=" N MET A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.557A pdb=" N TRP A 533 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 562 removed outlier: 3.960A pdb=" N PHE A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 558 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 601 removed outlier: 4.793A pdb=" N LEU A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.989A pdb=" N ALA A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 633 Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.916A pdb=" N LYS A 675 " --> pdb=" O ILE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 691 through 704 removed outlier: 3.917A pdb=" N GLN A 695 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 728 through 742 Processing helix chain 'C' and resid 2 through 17 removed outlier: 3.511A pdb=" N THR C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 35 removed outlier: 4.043A pdb=" N ARG C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET C 25 " --> pdb=" O ASP C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 removed outlier: 3.552A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 76 removed outlier: 4.479A pdb=" N GLN C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 77 through 80 removed outlier: 5.946A pdb=" N LYS C 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 81 through 96 removed outlier: 4.008A pdb=" N GLU C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.786A pdb=" N LYS C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 144 removed outlier: 3.706A pdb=" N GLN C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 164 removed outlier: 3.944A pdb=" N ASP C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 172 through 185 Proline residue: C 182 - end of helix removed outlier: 3.679A pdb=" N SER C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.791A pdb=" N GLU C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 268 removed outlier: 4.117A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N HIS C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ARG C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Proline residue: C 261 - end of helix Processing helix chain 'C' and resid 271 through 289 Processing helix chain 'C' and resid 296 through 309 removed outlier: 4.252A pdb=" N LYS C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 364 removed outlier: 4.230A pdb=" N VAL C 351 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 377 Processing helix chain 'C' and resid 377 through 384 Processing helix chain 'C' and resid 389 through 408 removed outlier: 4.005A pdb=" N GLN C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 4.309A pdb=" N MET C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.791A pdb=" N VAL C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 438 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 446 Processing helix chain 'C' and resid 449 through 467 Processing helix chain 'C' and resid 471 through 473 No H-bonds generated for 'chain 'C' and resid 471 through 473' Processing helix chain 'C' and resid 474 through 488 removed outlier: 3.795A pdb=" N LEU C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP C 488 " --> pdb=" O PHE C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 4.487A pdb=" N ARG C 496 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.888A pdb=" N PHE C 515 " --> pdb=" O PRO C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.548A pdb=" N VAL C 526 " --> pdb=" O LEU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 553 Processing helix chain 'C' and resid 563 through 580 removed outlier: 3.662A pdb=" N ALA C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 603 removed outlier: 3.838A pdb=" N LYS C 588 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 590 " --> pdb=" O GLU C 586 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C 591 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS C 594 " --> pdb=" O ARG C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 608 No H-bonds generated for 'chain 'C' and resid 606 through 608' Processing helix chain 'C' and resid 609 through 623 Processing helix chain 'C' and resid 626 through 640 Processing helix chain 'C' and resid 646 through 663 removed outlier: 4.554A pdb=" N ALA C 651 " --> pdb=" O GLN C 647 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N HIS C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 656 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 662 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 663 " --> pdb=" O SER C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 684 removed outlier: 3.821A pdb=" N LEU C 670 " --> pdb=" O ARG C 666 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 708 through 725 Processing helix chain 'C' and resid 727 through 731 removed outlier: 3.529A pdb=" N VAL C 730 " --> pdb=" O ALA C 727 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU C 731 " --> pdb=" O SER C 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 727 through 731' Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 740 through 745 removed outlier: 3.847A pdb=" N LEU C 744 " --> pdb=" O LEU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 755 removed outlier: 4.856A pdb=" N GLY C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 766 Processing helix chain 'C' and resid 775 through 782 Processing helix chain 'C' and resid 797 through 815 removed outlier: 3.571A pdb=" N ALA C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 815 " --> pdb=" O LEU C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 830 removed outlier: 4.298A pdb=" N SER C 821 " --> pdb=" O GLN C 817 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 822 " --> pdb=" O GLU C 818 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 830 " --> pdb=" O LEU C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 849 removed outlier: 3.757A pdb=" N LYS C 840 " --> pdb=" O SER C 836 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 841 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 845 " --> pdb=" O VAL C 841 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 849 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 853 through 859 removed outlier: 3.869A pdb=" N GLY C 857 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 869 removed outlier: 3.519A pdb=" N VAL C 865 " --> pdb=" O GLU C 861 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 867 " --> pdb=" O LYS C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 887 removed outlier: 3.737A pdb=" N ARG C 878 " --> pdb=" O SER C 874 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 887 " --> pdb=" O TYR C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 892 through 907 Proline residue: C 898 - end of helix removed outlier: 4.057A pdb=" N GLU C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 903 " --> pdb=" O PHE C 899 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE C 904 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 924 removed outlier: 3.767A pdb=" N ALA C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 947 removed outlier: 4.353A pdb=" N GLU C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP C 936 " --> pdb=" O PRO C 932 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 939 " --> pdb=" O GLU C 935 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 946 " --> pdb=" O PHE C 942 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY C 947 " --> pdb=" O GLN C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 965 removed outlier: 3.849A pdb=" N LYS C 962 " --> pdb=" O GLU C 958 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 963 " --> pdb=" O CYS C 959 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 965 " --> pdb=" O GLY C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 982 Proline residue: C 973 - end of helix Processing helix chain 'C' and resid 983 through 998 removed outlier: 3.593A pdb=" N ILE C 998 " --> pdb=" O VAL C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1017 removed outlier: 4.057A pdb=" N LYS C1010 " --> pdb=" O ASP C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1022 Processing helix chain 'C' and resid 1024 through 1041 removed outlier: 3.982A pdb=" N ARG C1028 " --> pdb=" O ASP C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1062 removed outlier: 3.798A pdb=" N ILE C1053 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Proline residue: C1055 - end of helix Processing helix chain 'C' and resid 1064 through 1066 No H-bonds generated for 'chain 'C' and resid 1064 through 1066' Processing helix chain 'C' and resid 1083 through 1099 removed outlier: 4.301A pdb=" N GLU C1099 " --> pdb=" O TYR C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1105 removed outlier: 6.090A pdb=" N GLY C1103 " --> pdb=" O SER C1100 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C1105 " --> pdb=" O LEU C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1118 Processing helix chain 'C' and resid 1121 through 1139 removed outlier: 4.034A pdb=" N THR C1137 " --> pdb=" O ALA C1133 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1160 removed outlier: 4.230A pdb=" N VAL C1143 " --> pdb=" O CYS C1139 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP C1148 " --> pdb=" O LEU C1144 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG C1149 " --> pdb=" O GLN C1145 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C1150 " --> pdb=" O ARG C1146 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU C1152 " --> pdb=" O ASP C1148 " (cutoff:3.500A) Proline residue: C1153 - end of helix Processing helix chain 'C' and resid 1167 through 1191 removed outlier: 3.813A pdb=" N PHE C1171 " --> pdb=" O VAL C1167 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C1191 " --> pdb=" O ALA C1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 1197 through 1210 removed outlier: 3.916A pdb=" N ASP C1202 " --> pdb=" O PRO C1198 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C1203 " --> pdb=" O ILE C1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1226 removed outlier: 3.531A pdb=" N PHE C1217 " --> pdb=" O LEU C1213 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C1219 " --> pdb=" O ALA C1215 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C1220 " --> pdb=" O LEU C1216 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C1221 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS C1222 " --> pdb=" O GLU C1218 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP C1223 " --> pdb=" O SER C1219 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C1224 " --> pdb=" O ILE C1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA2, first strand: chain 'C' and resid 1068 through 1070 862 hydrogen bonds defined for protein. 2562 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: 2.26 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4873 1.34 - 1.46: 2155 1.46 - 1.57: 7668 1.57 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 14829 Sorted by residual: bond pdb=" N MET C1017 " pdb=" CA MET C1017 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.88e+00 bond pdb=" CB PHE A 397 " pdb=" CG PHE A 397 " ideal model delta sigma weight residual 1.502 1.474 0.028 2.30e-02 1.89e+03 1.45e+00 bond pdb=" CG GLU C1092 " pdb=" CD GLU C1092 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.12e+00 bond pdb=" CD1 PHE A 397 " pdb=" CE1 PHE A 397 " ideal model delta sigma weight residual 1.382 1.350 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" C TRP A 533 " pdb=" N PRO A 534 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.21e-02 6.83e+03 1.07e+00 ... (remaining 14824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 19374 1.57 - 3.14: 494 3.14 - 4.71: 123 4.71 - 6.28: 45 6.28 - 7.85: 9 Bond angle restraints: 20045 Sorted by residual: angle pdb=" N VAL A 226 " pdb=" CA VAL A 226 " pdb=" C VAL A 226 " ideal model delta sigma weight residual 113.71 108.54 5.17 9.50e-01 1.11e+00 2.97e+01 angle pdb=" C LEU A 639 " pdb=" CA LEU A 639 " pdb=" CB LEU A 639 " ideal model delta sigma weight residual 115.89 110.64 5.25 1.32e+00 5.74e-01 1.58e+01 angle pdb=" N GLU C1092 " pdb=" CA GLU C1092 " pdb=" CB GLU C1092 " ideal model delta sigma weight residual 110.39 116.50 -6.11 1.66e+00 3.63e-01 1.35e+01 angle pdb=" N ALA C 756 " pdb=" CA ALA C 756 " pdb=" C ALA C 756 " ideal model delta sigma weight residual 114.39 109.11 5.28 1.45e+00 4.76e-01 1.32e+01 angle pdb=" C PHE C1091 " pdb=" N GLU C1092 " pdb=" CA GLU C1092 " ideal model delta sigma weight residual 120.72 114.84 5.88 1.67e+00 3.59e-01 1.24e+01 ... (remaining 20040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 8145 17.36 - 34.73: 830 34.73 - 52.09: 158 52.09 - 69.46: 27 69.46 - 86.82: 20 Dihedral angle restraints: 9180 sinusoidal: 3742 harmonic: 5438 Sorted by residual: dihedral pdb=" CA PHE C1016 " pdb=" C PHE C1016 " pdb=" N MET C1017 " pdb=" CA MET C1017 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS C 797 " pdb=" C HIS C 797 " pdb=" N LYS C 798 " pdb=" CA LYS C 798 " ideal model delta harmonic sigma weight residual -180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PRO C 563 " pdb=" C PRO C 563 " pdb=" N GLU C 564 " pdb=" CA GLU C 564 " ideal model delta harmonic sigma weight residual -180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 9177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1742 0.045 - 0.090: 486 0.090 - 0.135: 96 0.135 - 0.180: 8 0.180 - 0.224: 1 Chirality restraints: 2333 Sorted by residual: chirality pdb=" CB VAL C 263 " pdb=" CA VAL C 263 " pdb=" CG1 VAL C 263 " pdb=" CG2 VAL C 263 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA GLU A 238 " pdb=" N GLU A 238 " pdb=" C GLU A 238 " pdb=" CB GLU A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CB VAL C 79 " pdb=" CA VAL C 79 " pdb=" CG1 VAL C 79 " pdb=" CG2 VAL C 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 2330 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 746 " 0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 747 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 747 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 747 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 734 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO C 735 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 735 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 735 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 688 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO C 689 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 689 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 689 " 0.028 5.00e-02 4.00e+02 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3035 2.77 - 3.30: 16695 3.30 - 3.83: 24646 3.83 - 4.37: 27743 4.37 - 4.90: 43309 Nonbonded interactions: 115428 Sorted by model distance: nonbonded pdb=" O PHE A 155 " pdb=" OG1 THR A 159 " model vdw 2.235 3.040 nonbonded pdb=" OE2 GLU A 342 " pdb=" OG1 THR A 346 " model vdw 2.236 3.040 nonbonded pdb=" O GLU C 949 " pdb=" OG1 THR C 952 " model vdw 2.237 3.040 nonbonded pdb=" O GLN C1145 " pdb=" NH2 ARG C1149 " model vdw 2.241 3.120 nonbonded pdb=" O LEU C 305 " pdb=" NZ LYS C 309 " model vdw 2.244 3.120 ... (remaining 115423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14829 Z= 0.153 Angle : 0.676 7.853 20045 Z= 0.348 Chirality : 0.041 0.224 2333 Planarity : 0.005 0.083 2585 Dihedral : 14.880 86.820 5628 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.00 (0.21), residues: 1848 helix: 0.85 (0.15), residues: 1243 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 150 TYR 0.010 0.001 TYR A 558 PHE 0.029 0.001 PHE C1012 TRP 0.011 0.001 TRP A 63 HIS 0.009 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (14829) covalent geometry : angle 0.67595 / 0.35 (20045) hydrogen bonds : bond 0.15201 / 9.98 ( 862) hydrogen bonds : angle 5.98723 / 4.24 ( 2562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9682 (mmp) cc_final: 0.9296 (mmm) REVERT: A 213 LEU cc_start: 0.9255 (tp) cc_final: 0.8956 (tp) REVERT: A 434 ASP cc_start: 0.9328 (m-30) cc_final: 0.9095 (m-30) REVERT: A 536 TYR cc_start: 0.9192 (m-10) cc_final: 0.8964 (m-80) REVERT: C 15 MET cc_start: 0.9008 (mpp) cc_final: 0.8786 (mpp) REVERT: C 840 LYS cc_start: 0.9370 (mptt) cc_final: 0.8998 (mmtm) REVERT: C 1126 MET cc_start: 0.8834 (mpp) cc_final: 0.8599 (mpp) REVERT: C 1200 MET cc_start: 0.8698 (ppp) cc_final: 0.8331 (ppp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0816 time to fit residues: 22.8452 Evaluate side-chains 122 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 HIS ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.059916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.043879 restraints weight = 91681.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045241 restraints weight = 59670.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.046207 restraints weight = 43861.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046888 restraints weight = 35061.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047337 restraints weight = 29745.074| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14829 Z= 0.127 Angle : 0.640 7.835 20045 Z= 0.319 Chirality : 0.041 0.161 2333 Planarity : 0.005 0.078 2585 Dihedral : 4.395 40.935 1999 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.31 % Allowed : 6.64 % Favored : 93.05 % 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: -0.05 (0.21), residues: 1848 helix: 0.82 (0.15), residues: 1289 sheet: -1.14 (1.35), residues: 20 loop : -2.05 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 150 TYR 0.011 0.001 TYR A 453 PHE 0.022 0.001 PHE C 801 TRP 0.006 0.001 TRP A 63 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (14829) covalent geometry : angle 0.63998 / 0.32 (20045) hydrogen bonds : bond 0.04136 / 2.77 ( 862) hydrogen bonds : angle 4.64775 / 3.30 ( 2562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 180 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9663 (mmp) cc_final: 0.9323 (mmm) REVERT: A 213 LEU cc_start: 0.9278 (tp) cc_final: 0.8918 (tp) REVERT: A 434 ASP cc_start: 0.9345 (m-30) cc_final: 0.9101 (m-30) REVERT: A 536 TYR cc_start: 0.9112 (m-10) cc_final: 0.8910 (m-80) REVERT: C 15 MET cc_start: 0.8925 (mpp) cc_final: 0.8706 (mpp) REVERT: C 282 PHE cc_start: 0.9186 (m-80) cc_final: 0.8934 (m-80) REVERT: C 840 LYS cc_start: 0.9218 (mptt) cc_final: 0.8867 (mmtm) REVERT: C 1110 PHE cc_start: 0.8950 (m-80) cc_final: 0.8741 (m-80) REVERT: C 1126 MET cc_start: 0.8917 (mpp) cc_final: 0.8602 (mpp) REVERT: C 1200 MET cc_start: 0.8720 (ppp) cc_final: 0.8398 (ppp) outliers start: 5 outliers final: 3 residues processed: 183 average time/residue: 0.0825 time to fit residues: 25.1225 Evaluate side-chains 129 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN A 314 ASN C 310 HIS ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.058794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042592 restraints weight = 97542.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043951 restraints weight = 62612.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044907 restraints weight = 45784.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.045595 restraints weight = 36696.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046056 restraints weight = 31087.309| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14829 Z= 0.165 Angle : 0.652 6.970 20045 Z= 0.334 Chirality : 0.041 0.182 2333 Planarity : 0.005 0.072 2585 Dihedral : 4.466 41.672 1999 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.19 % Allowed : 6.07 % Favored : 93.74 % 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: -0.14 (0.20), residues: 1848 helix: 0.74 (0.15), residues: 1281 sheet: -0.00 (2.01), residues: 10 loop : -2.04 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1149 TYR 0.013 0.001 TYR C 912 PHE 0.055 0.002 PHE C1012 TRP 0.013 0.001 TRP A 63 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (14829) covalent geometry : angle 0.65212 / 0.33 (20045) hydrogen bonds : bond 0.03871 / 2.58 ( 862) hydrogen bonds : angle 4.73014 / 3.37 ( 2562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9644 (mmp) cc_final: 0.9237 (mmm) REVERT: A 213 LEU cc_start: 0.9339 (tp) cc_final: 0.9023 (tp) REVERT: A 434 ASP cc_start: 0.9334 (m-30) cc_final: 0.9100 (m-30) REVERT: C 282 PHE cc_start: 0.9235 (m-80) cc_final: 0.8960 (m-80) REVERT: C 527 MET cc_start: 0.9155 (mpp) cc_final: 0.8713 (ptp) REVERT: C 840 LYS cc_start: 0.9316 (mptt) cc_final: 0.8949 (mmtm) REVERT: C 1126 MET cc_start: 0.8933 (mpp) cc_final: 0.8605 (mpp) REVERT: C 1200 MET cc_start: 0.8738 (ppp) cc_final: 0.8423 (ppp) outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.0869 time to fit residues: 24.6008 Evaluate side-chains 124 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 137 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044201 restraints weight = 94040.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045578 restraints weight = 60906.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.046559 restraints weight = 44721.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047254 restraints weight = 35752.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047746 restraints weight = 30242.607| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14829 Z= 0.120 Angle : 0.651 12.663 20045 Z= 0.320 Chirality : 0.041 0.175 2333 Planarity : 0.005 0.075 2585 Dihedral : 4.407 41.189 1999 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.25 % Allowed : 4.20 % Favored : 95.55 % 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: -0.05 (0.20), residues: 1848 helix: 0.81 (0.15), residues: 1285 sheet: -1.17 (1.38), residues: 20 loop : -2.02 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 742 TYR 0.008 0.001 TYR A 558 PHE 0.032 0.002 PHE A 689 TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (14829) covalent geometry : angle 0.65149 / 0.32 (20045) hydrogen bonds : bond 0.03509 / 2.36 ( 862) hydrogen bonds : angle 4.47652 / 3.18 ( 2562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9663 (mmp) cc_final: 0.9327 (mmm) REVERT: A 201 GLU cc_start: 0.9058 (mp0) cc_final: 0.8822 (tm-30) REVERT: A 213 LEU cc_start: 0.9383 (tp) cc_final: 0.9039 (tp) REVERT: A 342 GLU cc_start: 0.8941 (tp30) cc_final: 0.8723 (tm-30) REVERT: A 434 ASP cc_start: 0.9387 (m-30) cc_final: 0.9159 (m-30) REVERT: A 475 MET cc_start: 0.8569 (tmm) cc_final: 0.8289 (tmm) REVERT: A 536 TYR cc_start: 0.9184 (m-10) cc_final: 0.8831 (m-80) REVERT: C 282 PHE cc_start: 0.9315 (m-80) cc_final: 0.8967 (m-80) REVERT: C 347 MET cc_start: 0.8564 (mmp) cc_final: 0.8271 (mmm) REVERT: C 350 LYS cc_start: 0.9603 (mttt) cc_final: 0.9378 (mttm) REVERT: C 840 LYS cc_start: 0.9308 (mptt) cc_final: 0.8956 (mmtm) REVERT: C 1110 PHE cc_start: 0.9027 (m-80) cc_final: 0.8739 (m-80) REVERT: C 1126 MET cc_start: 0.8951 (mpp) cc_final: 0.8616 (mpp) REVERT: C 1200 MET cc_start: 0.8850 (ppp) cc_final: 0.8570 (ppp) outliers start: 4 outliers final: 2 residues processed: 189 average time/residue: 0.0854 time to fit residues: 26.3832 Evaluate side-chains 134 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 71 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 134 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 182 optimal weight: 0.0020 chunk 138 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 590 GLN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.060589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044237 restraints weight = 92777.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045717 restraints weight = 58681.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.046761 restraints weight = 42382.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047486 restraints weight = 33447.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047957 restraints weight = 28100.882| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14829 Z= 0.116 Angle : 0.651 8.015 20045 Z= 0.320 Chirality : 0.041 0.194 2333 Planarity : 0.005 0.074 2585 Dihedral : 4.359 40.287 1999 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % 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: -0.06 (0.20), residues: 1848 helix: 0.82 (0.15), residues: 1286 sheet: -1.13 (1.39), residues: 20 loop : -2.08 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.011 0.001 TYR A 453 PHE 0.023 0.001 PHE C 801 TRP 0.008 0.001 TRP A 139 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (14829) covalent geometry : angle 0.65063 / 0.32 (20045) hydrogen bonds : bond 0.03261 / 2.17 ( 862) hydrogen bonds : angle 4.44943 / 3.17 ( 2562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9621 (mmp) cc_final: 0.9241 (mmm) REVERT: A 213 LEU cc_start: 0.9276 (tp) cc_final: 0.8954 (tp) REVERT: A 434 ASP cc_start: 0.9322 (m-30) cc_final: 0.9101 (m-30) REVERT: A 536 TYR cc_start: 0.9119 (m-10) cc_final: 0.8837 (m-80) REVERT: A 686 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8966 (pm20) REVERT: C 282 PHE cc_start: 0.9226 (m-80) cc_final: 0.8961 (m-80) REVERT: C 347 MET cc_start: 0.8475 (mmp) cc_final: 0.8188 (mmm) REVERT: C 527 MET cc_start: 0.9113 (mpp) cc_final: 0.8750 (ppp) REVERT: C 840 LYS cc_start: 0.9275 (mptt) cc_final: 0.8932 (mmtm) REVERT: C 1126 MET cc_start: 0.8896 (mpp) cc_final: 0.8604 (mpp) REVERT: C 1200 MET cc_start: 0.8887 (ppp) cc_final: 0.8630 (ppp) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.0935 time to fit residues: 28.0505 Evaluate side-chains 131 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 23 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 111 optimal weight: 0.1980 chunk 77 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 590 GLN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.060615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044511 restraints weight = 90849.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.045934 restraints weight = 58495.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.046941 restraints weight = 42659.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047655 restraints weight = 33843.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048155 restraints weight = 28499.362| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14829 Z= 0.115 Angle : 0.656 8.636 20045 Z= 0.321 Chirality : 0.041 0.167 2333 Planarity : 0.005 0.074 2585 Dihedral : 4.325 40.126 1999 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.13 % Allowed : 2.69 % Favored : 97.18 % 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: -0.05 (0.20), residues: 1848 helix: 0.84 (0.15), residues: 1272 sheet: -1.14 (1.39), residues: 20 loop : -2.03 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1149 TYR 0.009 0.001 TYR C 566 PHE 0.025 0.001 PHE A 153 TRP 0.007 0.001 TRP C 553 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (14829) covalent geometry : angle 0.65617 / 0.32 (20045) hydrogen bonds : bond 0.03205 / 2.13 ( 862) hydrogen bonds : angle 4.41452 / 3.15 ( 2562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9630 (mmp) cc_final: 0.9249 (mmm) REVERT: A 213 LEU cc_start: 0.9273 (tp) cc_final: 0.8964 (tp) REVERT: A 434 ASP cc_start: 0.9325 (m-30) cc_final: 0.9094 (m-30) REVERT: A 735 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8550 (tpp80) REVERT: C 282 PHE cc_start: 0.9226 (m-80) cc_final: 0.8944 (m-80) REVERT: C 527 MET cc_start: 0.9137 (mpp) cc_final: 0.8692 (ptp) REVERT: C 708 MET cc_start: 0.8137 (mmp) cc_final: 0.7133 (mtm) REVERT: C 840 LYS cc_start: 0.9295 (mptt) cc_final: 0.8982 (mmtm) REVERT: C 842 LEU cc_start: 0.9698 (mm) cc_final: 0.9427 (pp) REVERT: C 1110 PHE cc_start: 0.8953 (m-80) cc_final: 0.8690 (m-80) REVERT: C 1126 MET cc_start: 0.8872 (mpp) cc_final: 0.8542 (mpp) REVERT: C 1200 MET cc_start: 0.8906 (ppp) cc_final: 0.8642 (ppp) outliers start: 2 outliers final: 1 residues processed: 189 average time/residue: 0.0961 time to fit residues: 29.5007 Evaluate side-chains 136 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 590 GLN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.060681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044572 restraints weight = 94049.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046002 restraints weight = 60567.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.047002 restraints weight = 44284.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.047656 restraints weight = 35305.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048185 restraints weight = 29977.192| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14829 Z= 0.120 Angle : 0.668 8.573 20045 Z= 0.331 Chirality : 0.042 0.213 2333 Planarity : 0.005 0.083 2585 Dihedral : 4.335 40.024 1999 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.06 % Allowed : 1.69 % Favored : 98.25 % 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: -0.02 (0.20), residues: 1848 helix: 0.85 (0.15), residues: 1279 sheet: -1.15 (1.38), residues: 20 loop : -2.01 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 909 TYR 0.017 0.001 TYR C 912 PHE 0.045 0.001 PHE C 373 TRP 0.014 0.001 TRP C 938 HIS 0.006 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14829) covalent geometry : angle 0.66834 / 0.33 (20045) hydrogen bonds : bond 0.03262 / 2.14 ( 862) hydrogen bonds : angle 4.49639 / 3.22 ( 2562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9625 (mmp) cc_final: 0.9232 (mmm) REVERT: A 213 LEU cc_start: 0.9264 (tp) cc_final: 0.8972 (tp) REVERT: A 434 ASP cc_start: 0.9297 (m-30) cc_final: 0.9091 (m-30) REVERT: C 282 PHE cc_start: 0.9216 (m-80) cc_final: 0.8956 (m-80) REVERT: C 527 MET cc_start: 0.9115 (mpp) cc_final: 0.8675 (ptp) REVERT: C 708 MET cc_start: 0.8040 (mmp) cc_final: 0.7153 (mtm) REVERT: C 840 LYS cc_start: 0.9314 (mptt) cc_final: 0.8956 (mmtm) REVERT: C 1126 MET cc_start: 0.8890 (mpp) cc_final: 0.8540 (mpp) REVERT: C 1200 MET cc_start: 0.8903 (ppp) cc_final: 0.8644 (ppp) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.0922 time to fit residues: 28.1469 Evaluate side-chains 131 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 140 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 590 GLN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.059582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043601 restraints weight = 91945.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044996 restraints weight = 59154.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.045964 restraints weight = 43171.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.046672 restraints weight = 34300.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.047144 restraints weight = 28928.507| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14829 Z= 0.137 Angle : 0.670 8.317 20045 Z= 0.337 Chirality : 0.042 0.188 2333 Planarity : 0.005 0.073 2585 Dihedral : 4.361 40.323 1999 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.06 % Allowed : 1.44 % Favored : 98.50 % 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: 0.01 (0.20), residues: 1848 helix: 0.88 (0.15), residues: 1285 sheet: -1.29 (1.36), residues: 20 loop : -2.06 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 80 TYR 0.007 0.001 TYR A 558 PHE 0.049 0.002 PHE C 373 TRP 0.033 0.002 TRP C 938 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (14829) covalent geometry : angle 0.67050 / 0.34 (20045) hydrogen bonds : bond 0.03348 / 2.22 ( 862) hydrogen bonds : angle 4.55242 / 3.28 ( 2562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9631 (mmp) cc_final: 0.9238 (mmm) REVERT: A 213 LEU cc_start: 0.9291 (tp) cc_final: 0.8999 (tp) REVERT: A 434 ASP cc_start: 0.9318 (m-30) cc_final: 0.9095 (m-30) REVERT: C 282 PHE cc_start: 0.9235 (m-80) cc_final: 0.8961 (m-80) REVERT: C 527 MET cc_start: 0.9131 (mpp) cc_final: 0.8698 (ptp) REVERT: C 708 MET cc_start: 0.8089 (mmp) cc_final: 0.7460 (mtm) REVERT: C 840 LYS cc_start: 0.9330 (mptt) cc_final: 0.8966 (mmtm) REVERT: C 995 LYS cc_start: 0.9355 (tttt) cc_final: 0.9054 (tptt) REVERT: C 1110 PHE cc_start: 0.8949 (m-80) cc_final: 0.8705 (m-80) REVERT: C 1126 MET cc_start: 0.8889 (mpp) cc_final: 0.8562 (mpp) REVERT: C 1200 MET cc_start: 0.8865 (ppp) cc_final: 0.8601 (ppp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0900 time to fit residues: 26.2147 Evaluate side-chains 131 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 6 optimal weight: 0.0970 chunk 66 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 590 GLN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** 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 = 0.3372 r_free = 0.3372 target = 0.059977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043725 restraints weight = 93816.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.045179 restraints weight = 59400.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.046202 restraints weight = 42999.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046919 restraints weight = 34024.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.047429 restraints weight = 28647.704| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14829 Z= 0.123 Angle : 0.680 8.693 20045 Z= 0.339 Chirality : 0.042 0.216 2333 Planarity : 0.005 0.073 2585 Dihedral : 4.363 40.065 1999 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.06 % Allowed : 0.81 % Favored : 99.12 % 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: 0.05 (0.20), residues: 1848 helix: 0.90 (0.15), residues: 1281 sheet: -1.22 (1.37), residues: 20 loop : -1.98 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.013 0.001 TYR C 912 PHE 0.043 0.001 PHE C 373 TRP 0.032 0.002 TRP C 938 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (14829) covalent geometry : angle 0.67980 / 0.34 (20045) hydrogen bonds : bond 0.03330 / 2.19 ( 862) hydrogen bonds : angle 4.54969 / 3.26 ( 2562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9613 (mmp) cc_final: 0.9231 (mmm) REVERT: A 213 LEU cc_start: 0.9290 (tp) cc_final: 0.8994 (tp) REVERT: A 434 ASP cc_start: 0.9292 (m-30) cc_final: 0.9080 (m-30) REVERT: C 282 PHE cc_start: 0.9193 (m-80) cc_final: 0.8932 (m-80) REVERT: C 527 MET cc_start: 0.9110 (mpp) cc_final: 0.8673 (ptp) REVERT: C 708 MET cc_start: 0.7988 (mmp) cc_final: 0.7402 (mtm) REVERT: C 740 LEU cc_start: 0.9377 (pt) cc_final: 0.9143 (mp) REVERT: C 806 ARG cc_start: 0.9418 (ttm170) cc_final: 0.8985 (mtm-85) REVERT: C 840 LYS cc_start: 0.9308 (mptt) cc_final: 0.8957 (mmtm) REVERT: C 995 LYS cc_start: 0.9329 (tttt) cc_final: 0.9032 (tptt) REVERT: C 1017 MET cc_start: 0.7463 (mpp) cc_final: 0.7255 (mpp) REVERT: C 1110 PHE cc_start: 0.8928 (m-80) cc_final: 0.8719 (m-80) REVERT: C 1126 MET cc_start: 0.8903 (mpp) cc_final: 0.8570 (mpp) REVERT: C 1200 MET cc_start: 0.8854 (ppp) cc_final: 0.8607 (ppp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.0861 time to fit residues: 25.9356 Evaluate side-chains 130 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 590 GLN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** 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 = 0.3381 r_free = 0.3381 target = 0.060440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044365 restraints weight = 90724.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045778 restraints weight = 58275.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046779 restraints weight = 42559.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.047485 restraints weight = 33776.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047999 restraints weight = 28457.197| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14829 Z= 0.120 Angle : 0.689 8.983 20045 Z= 0.340 Chirality : 0.042 0.204 2333 Planarity : 0.005 0.073 2585 Dihedral : 4.359 39.651 1999 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.62 % 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: 0.06 (0.20), residues: 1848 helix: 0.91 (0.15), residues: 1273 sheet: -1.19 (1.38), residues: 20 loop : -1.94 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 909 TYR 0.008 0.001 TYR C 774 PHE 0.041 0.001 PHE C 373 TRP 0.031 0.002 TRP C 938 HIS 0.005 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (14829) covalent geometry : angle 0.68926 / 0.34 (20045) hydrogen bonds : bond 0.03222 / 2.15 ( 862) hydrogen bonds : angle 4.55902 / 3.27 ( 2562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9604 (mmp) cc_final: 0.9220 (mmm) REVERT: A 213 LEU cc_start: 0.9255 (tp) cc_final: 0.8957 (tp) REVERT: A 434 ASP cc_start: 0.9283 (m-30) cc_final: 0.9070 (m-30) REVERT: C 282 PHE cc_start: 0.9152 (m-80) cc_final: 0.8880 (m-80) REVERT: C 527 MET cc_start: 0.9115 (mpp) cc_final: 0.8696 (ptp) REVERT: C 708 MET cc_start: 0.7918 (mmp) cc_final: 0.7370 (mtm) REVERT: C 740 LEU cc_start: 0.9317 (pt) cc_final: 0.9099 (mp) REVERT: C 806 ARG cc_start: 0.9411 (ttm170) cc_final: 0.8994 (mtm-85) REVERT: C 840 LYS cc_start: 0.9308 (mptt) cc_final: 0.8960 (mmtm) REVERT: C 995 LYS cc_start: 0.9315 (tttt) cc_final: 0.8999 (tptt) REVERT: C 1092 GLU cc_start: 0.9389 (mp0) cc_final: 0.9135 (pm20) REVERT: C 1126 MET cc_start: 0.8880 (mpp) cc_final: 0.8554 (mpp) REVERT: C 1200 MET cc_start: 0.8887 (ppp) cc_final: 0.8648 (ppp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.0793 time to fit residues: 24.2067 Evaluate side-chains 135 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 590 GLN C 296 HIS ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044383 restraints weight = 92561.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045821 restraints weight = 59556.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.046843 restraints weight = 43446.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.047544 restraints weight = 34468.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048002 restraints weight = 29190.857| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14829 Z= 0.119 Angle : 0.688 8.940 20045 Z= 0.340 Chirality : 0.042 0.192 2333 Planarity : 0.005 0.073 2585 Dihedral : 4.332 39.385 1999 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.62 % 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: 0.05 (0.20), residues: 1848 helix: 0.88 (0.15), residues: 1281 sheet: -1.14 (1.38), residues: 20 loop : -1.94 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 909 TYR 0.015 0.001 TYR C 912 PHE 0.040 0.001 PHE C 373 TRP 0.030 0.002 TRP C 938 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14829) covalent geometry : angle 0.68811 / 0.34 (20045) hydrogen bonds : bond 0.03222 / 2.13 ( 862) hydrogen bonds : angle 4.55140 / 3.26 ( 2562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.73 seconds wall clock time: 40 minutes 0.98 seconds (2400.98 seconds total)