Starting phenix.real_space_refine on Wed Mar 4 15:47:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zbw_14594/03_2026/7zbw_14594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zbw_14594/03_2026/7zbw_14594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zbw_14594/03_2026/7zbw_14594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zbw_14594/03_2026/7zbw_14594.map" model { file = "/net/cci-nas-00/data/ceres_data/7zbw_14594/03_2026/7zbw_14594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zbw_14594/03_2026/7zbw_14594.cif" } resolution = 3.5 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= 0.002 sd= 0.028 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 75 5.16 5 C 9364 2.51 5 N 2551 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14784 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5760 Classifications: {'peptide': 709} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 697} Chain breaks: 5 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 98 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "D" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6320 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 38, 'TRANS': 809} Chain breaks: 6 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 7, 'TYR:plan': 3, 'GLU:plan': 9, 'PHE:plan': 2, 'HIS:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 144 Chain: "F" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1696 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 824 Unresolved non-hydrogen angles: 1056 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 13, 'GLN:plan1': 15, 'ASP:plan': 13, 'ASN:plan1': 14, 'HIS:plan': 10, 'PHE:plan': 12, 'TRP:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 423 Chain: "S" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 910 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 3.04, per 1000 atoms: 0.21 Number of scatterers: 14784 At special positions: 0 Unit cell: (160.026, 147.258, 121.722, 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 75 16.00 O 2794 8.00 N 2551 7.00 C 9364 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 673.2 milliseconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 71.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'C' and resid 16 through 32 removed outlier: 4.197A pdb=" N ILE C 20 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.741A pdb=" N HIS C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 105 removed outlier: 4.228A pdb=" N TYR C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.671A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 192 removed outlier: 3.574A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 4.240A pdb=" N ILE C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 255 removed outlier: 3.547A pdb=" N GLU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.786A pdb=" N TYR C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.918A pdb=" N THR C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 328 removed outlier: 4.137A pdb=" N ARG C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 356 removed outlier: 4.111A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.966A pdb=" N LEU C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 361' Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.600A pdb=" N VAL C 370 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 377 " --> pdb=" O VAL C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 404 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.628A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 removed outlier: 3.516A pdb=" N ASP C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 4.127A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.679A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 525 removed outlier: 4.163A pdb=" N LYS C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 622 through 630 removed outlier: 3.752A pdb=" N ASP C 627 " --> pdb=" O GLN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 688 through 720 removed outlier: 4.129A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 697 " --> pdb=" O LYS C 693 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 698 " --> pdb=" O GLN C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 19 through 34 Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.901A pdb=" N VAL D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 78 removed outlier: 3.951A pdb=" N LEU D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.255A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 95 removed outlier: 4.089A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.745A pdb=" N LYS D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 removed outlier: 3.956A pdb=" N LEU D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.774A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 4.253A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 removed outlier: 4.021A pdb=" N THR D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 Proline residue: D 258 - end of helix removed outlier: 3.508A pdb=" N CYS D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.645A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 345 through 364 removed outlier: 4.360A pdb=" N VAL D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.122A pdb=" N PHE D 371 " --> pdb=" O MET D 367 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) Proline residue: D 377 - end of helix Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 390 through 406 removed outlier: 3.807A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 431 removed outlier: 3.698A pdb=" N GLN D 431 " --> pdb=" O MET D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.846A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 3.546A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 490 through 507 removed outlier: 3.666A pdb=" N ASN D 507 " --> pdb=" O VAL D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix removed outlier: 3.819A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.566A pdb=" N GLU D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 577 removed outlier: 3.619A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 601 Processing helix chain 'D' and resid 606 through 618 removed outlier: 4.627A pdb=" N ASN D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.524A pdb=" N THR D 628 " --> pdb=" O THR D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 658 removed outlier: 4.508A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 682 through 685 Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.556A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 701 removed outlier: 4.206A pdb=" N LEU D 700 " --> pdb=" O GLU D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.724A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 731 removed outlier: 4.241A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER D 731 " --> pdb=" O SER D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 744 removed outlier: 3.727A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 766 removed outlier: 3.914A pdb=" N LEU D 752 " --> pdb=" O GLN D 748 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER D 753 " --> pdb=" O GLY D 749 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 780 Processing helix chain 'D' and resid 780 through 786 removed outlier: 3.899A pdb=" N TYR D 784 " --> pdb=" O THR D 780 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN D 786 " --> pdb=" O PRO D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 810 removed outlier: 4.180A pdb=" N TYR D 796 " --> pdb=" O HIS D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 823 removed outlier: 3.769A pdb=" N GLN D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 846 Processing helix chain 'D' and resid 856 through 866 removed outlier: 4.027A pdb=" N SER D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 removed outlier: 3.720A pdb=" N LYS D 873 " --> pdb=" O SER D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 902 Processing helix chain 'D' and resid 906 through 919 Processing helix chain 'F' and resid 101 through 111 removed outlier: 3.960A pdb=" N LEU F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS F 111 " --> pdb=" O GLY F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 124 through 132 removed outlier: 4.092A pdb=" N LEU F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER F 132 " --> pdb=" O TYR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 removed outlier: 4.000A pdb=" N GLN F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 219 through 227 Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.753A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 removed outlier: 3.579A pdb=" N GLU F 358 " --> pdb=" O GLU F 355 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 359 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 383 removed outlier: 4.175A pdb=" N LEU F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 23 removed outlier: 3.601A pdb=" N GLN S 23 " --> pdb=" O ILE S 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 20 through 23' Processing helix chain 'S' and resid 24 through 33 Processing helix chain 'S' and resid 53 through 65 Processing helix chain 'S' and resid 87 through 94 Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 128 Processing helix chain 'S' and resid 131 through 139 removed outlier: 3.554A pdb=" N ILE S 135 " --> pdb=" O THR S 131 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG S 136 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS S 137 " --> pdb=" O GLU S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 157 Processing sheet with id=AA1, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.335A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C 588 " --> pdb=" O ALA C 603 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA C 603 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 600 " --> pdb=" O VAL C 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 620 through 621 Processing sheet with id=AA3, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA4, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.541A pdb=" N ASP F 187 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA6, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AA7, first strand: chain 'F' and resid 339 through 341 removed outlier: 7.086A pdb=" N LEU F 340 " --> pdb=" O GLN F 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 13 through 17 removed outlier: 3.935A pdb=" N LEU S 6 " --> pdb=" O PHE S 14 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE S 4 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL S 45 " --> pdb=" O LYS S 5 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2742 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: 2.38 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4044 1.33 - 1.45: 2145 1.45 - 1.57: 8693 1.57 - 1.69: 0 1.69 - 1.81: 113 Bond restraints: 14995 Sorted by residual: bond pdb=" CG LEU F 117 " pdb=" CD2 LEU F 117 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CB ARG D 386 " pdb=" CG ARG D 386 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CA THR D 562 " pdb=" C THR D 562 " ideal model delta sigma weight residual 1.524 1.534 -0.011 1.26e-02 6.30e+03 7.15e-01 bond pdb=" CD GLN C 121 " pdb=" OE1 GLN C 121 " ideal model delta sigma weight residual 1.231 1.215 0.016 1.90e-02 2.77e+03 6.95e-01 bond pdb=" CG LEU C 116 " pdb=" CD2 LEU C 116 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.91e-01 ... (remaining 14990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 20025 1.72 - 3.45: 273 3.45 - 5.17: 49 5.17 - 6.90: 14 6.90 - 8.62: 1 Bond angle restraints: 20362 Sorted by residual: angle pdb=" C ARG C 401 " pdb=" N PHE C 402 " pdb=" CA PHE C 402 " ideal model delta sigma weight residual 122.06 116.15 5.91 1.86e+00 2.89e-01 1.01e+01 angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.48 -5.94 1.91e+00 2.74e-01 9.69e+00 angle pdb=" N GLU D 33 " pdb=" CA GLU D 33 " pdb=" CB GLU D 33 " ideal model delta sigma weight residual 110.16 114.55 -4.39 1.48e+00 4.57e-01 8.80e+00 angle pdb=" C VAL C 277 " pdb=" N TYR C 278 " pdb=" CA TYR C 278 " ideal model delta sigma weight residual 122.54 117.16 5.38 1.82e+00 3.02e-01 8.75e+00 angle pdb=" CA LYS D 133 " pdb=" CB LYS D 133 " pdb=" CG LYS D 133 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.63e+00 ... (remaining 20357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8328 17.96 - 35.91: 692 35.91 - 53.87: 108 53.87 - 71.83: 14 71.83 - 89.78: 14 Dihedral angle restraints: 9156 sinusoidal: 3236 harmonic: 5920 Sorted by residual: dihedral pdb=" CA ASP C 427 " pdb=" CB ASP C 427 " pdb=" CG ASP C 427 " pdb=" OD1 ASP C 427 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU C 210 " pdb=" CG GLU C 210 " pdb=" CD GLU C 210 " pdb=" OE1 GLU C 210 " ideal model delta sinusoidal sigma weight residual 0.00 89.78 -89.78 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG C 473 " pdb=" CD ARG C 473 " pdb=" NE ARG C 473 " pdb=" CZ ARG C 473 " ideal model delta sinusoidal sigma weight residual 90.00 133.91 -43.91 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 9153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1919 0.046 - 0.092: 468 0.092 - 0.139: 75 0.139 - 0.185: 2 0.185 - 0.231: 1 Chirality restraints: 2465 Sorted by residual: chirality pdb=" CB VAL D 79 " pdb=" CA VAL D 79 " pdb=" CG1 VAL D 79 " pdb=" CG2 VAL D 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA GLN C 121 " pdb=" N GLN C 121 " pdb=" C GLN C 121 " pdb=" CB GLN C 121 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA THR D 562 " pdb=" N THR D 562 " pdb=" C THR D 562 " pdb=" CB THR D 562 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2462 not shown) Planarity restraints: 2606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 131 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO S 132 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO S 132 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO S 132 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 473 " 0.038 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO D 474 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 474 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 474 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 652 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO D 653 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 653 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 653 " -0.031 5.00e-02 4.00e+02 ... (remaining 2603 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 310 2.71 - 3.26: 14936 3.26 - 3.80: 22924 3.80 - 4.35: 26281 4.35 - 4.90: 45742 Nonbonded interactions: 110193 Sorted by model distance: nonbonded pdb=" NZ LYS D 193 " pdb=" OE1 GLN D 236 " model vdw 2.162 3.120 nonbonded pdb=" OH TYR C 244 " pdb=" OE2 GLU C 271 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR D 372 " pdb=" OG1 THR D 405 " model vdw 2.255 3.040 nonbonded pdb=" O ASN C 386 " pdb=" ND2 ASN C 386 " model vdw 2.268 3.120 nonbonded pdb=" ND2 ASN C 518 " pdb=" O ILE C 537 " model vdw 2.282 3.120 ... (remaining 110188 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: 2.990 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 0.035 14995 Z= 0.134 Angle : 0.536 8.624 20362 Z= 0.284 Chirality : 0.039 0.231 2465 Planarity : 0.004 0.087 2606 Dihedral : 13.851 89.785 5286 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1976 helix: 2.02 (0.15), residues: 1287 sheet: -2.92 (0.78), residues: 35 loop : -1.14 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 506 TYR 0.018 0.001 TYR C 278 PHE 0.019 0.001 PHE C 402 TRP 0.023 0.001 TRP S 61 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00298 (14995) covalent geometry : angle 0.53608 (20362) hydrogen bonds : bond 0.13033 ( 925) hydrogen bonds : angle 4.75489 ( 2742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: C 225 LEU cc_start: 0.8560 (mt) cc_final: 0.8316 (mt) REVERT: C 229 LYS cc_start: 0.8095 (tttm) cc_final: 0.7892 (mtpp) REVERT: C 285 ASP cc_start: 0.7712 (p0) cc_final: 0.7390 (p0) REVERT: C 302 ILE cc_start: 0.8574 (tt) cc_final: 0.8311 (pt) REVERT: C 706 ASP cc_start: 0.6971 (m-30) cc_final: 0.6718 (m-30) REVERT: C 724 VAL cc_start: 0.8043 (t) cc_final: 0.7762 (p) REVERT: C 743 LYS cc_start: 0.8052 (mttp) cc_final: 0.7660 (ttmm) REVERT: D 51 LYS cc_start: 0.7206 (tptp) cc_final: 0.6724 (tptp) REVERT: D 221 GLU cc_start: 0.6765 (tp30) cc_final: 0.6530 (tp30) REVERT: D 228 MET cc_start: 0.7752 (ppp) cc_final: 0.7507 (tmm) REVERT: D 388 GLU cc_start: 0.6585 (mp0) cc_final: 0.6378 (mp0) REVERT: D 444 LYS cc_start: 0.8071 (mttm) cc_final: 0.7779 (mtpp) REVERT: D 446 LYS cc_start: 0.8159 (mppt) cc_final: 0.7836 (mppt) REVERT: D 518 GLN cc_start: 0.7648 (tp40) cc_final: 0.7143 (tp40) REVERT: D 538 GLU cc_start: 0.7409 (tp30) cc_final: 0.7175 (tp30) REVERT: D 691 ASP cc_start: 0.6900 (p0) cc_final: 0.6659 (p0) REVERT: D 703 GLU cc_start: 0.7282 (pp20) cc_final: 0.6783 (pp20) REVERT: D 737 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6965 (mm-30) REVERT: D 793 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7242 (mtmt) REVERT: D 797 TYR cc_start: 0.7019 (m-80) cc_final: 0.6508 (m-80) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.1220 time to fit residues: 58.6974 Evaluate side-chains 314 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.2980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN D 434 ASN D 442 GLN D 472 HIS D 662 ASN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123798 restraints weight = 24391.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127162 restraints weight = 11516.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129379 restraints weight = 6730.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130496 restraints weight = 4562.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131503 restraints weight = 3586.256| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14995 Z= 0.108 Angle : 0.494 7.047 20362 Z= 0.260 Chirality : 0.037 0.146 2465 Planarity : 0.004 0.064 2606 Dihedral : 3.541 15.855 2117 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.96 % Allowed : 8.88 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1976 helix: 2.13 (0.15), residues: 1306 sheet: -3.25 (0.71), residues: 45 loop : -1.05 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 406 TYR 0.019 0.001 TYR C 278 PHE 0.030 0.001 PHE C 402 TRP 0.013 0.001 TRP S 61 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00226 (14995) covalent geometry : angle 0.49413 (20362) hydrogen bonds : bond 0.03860 ( 925) hydrogen bonds : angle 3.86284 ( 2742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 322 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: C 95 PHE cc_start: 0.8178 (t80) cc_final: 0.7884 (t80) REVERT: C 121 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: C 285 ASP cc_start: 0.7615 (p0) cc_final: 0.7284 (p0) REVERT: C 301 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: C 302 ILE cc_start: 0.8513 (tt) cc_final: 0.8255 (pt) REVERT: C 706 ASP cc_start: 0.6928 (m-30) cc_final: 0.6655 (m-30) REVERT: C 743 LYS cc_start: 0.8095 (mttp) cc_final: 0.7820 (ttmm) REVERT: D 51 LYS cc_start: 0.7076 (tptp) cc_final: 0.6622 (tptp) REVERT: D 63 GLU cc_start: 0.7219 (mp0) cc_final: 0.6732 (mp0) REVERT: D 344 ASP cc_start: 0.7452 (t0) cc_final: 0.7092 (t70) REVERT: D 444 LYS cc_start: 0.8042 (mttm) cc_final: 0.7784 (mtpp) REVERT: D 446 LYS cc_start: 0.8164 (mppt) cc_final: 0.7848 (mppt) REVERT: D 518 GLN cc_start: 0.7609 (tp40) cc_final: 0.7133 (tp40) REVERT: D 614 ILE cc_start: 0.8280 (mm) cc_final: 0.8036 (tp) REVERT: D 703 GLU cc_start: 0.7272 (pp20) cc_final: 0.6907 (pp20) REVERT: D 793 LYS cc_start: 0.7405 (mtmt) cc_final: 0.6744 (mtmt) REVERT: D 797 TYR cc_start: 0.6451 (m-80) cc_final: 0.6189 (m-80) REVERT: F 127 TRP cc_start: 0.7861 (m-10) cc_final: 0.7623 (m-10) REVERT: S 31 LEU cc_start: 0.8663 (mt) cc_final: 0.8395 (mp) REVERT: S 57 LYS cc_start: 0.7896 (mppt) cc_final: 0.7588 (mmtm) outliers start: 14 outliers final: 7 residues processed: 326 average time/residue: 0.1258 time to fit residues: 58.3789 Evaluate side-chains 314 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 305 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 135 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 21 optimal weight: 1.9990 chunk 177 optimal weight: 50.0000 chunk 186 optimal weight: 7.9990 chunk 116 optimal weight: 0.4980 chunk 129 optimal weight: 0.4980 chunk 191 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 194 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 143 HIS C 253 GLN C 293 GLN D 442 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.150897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122790 restraints weight = 24638.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126134 restraints weight = 11713.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128155 restraints weight = 6877.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129591 restraints weight = 4749.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130505 restraints weight = 3636.216| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14995 Z= 0.112 Angle : 0.484 7.064 20362 Z= 0.255 Chirality : 0.037 0.142 2465 Planarity : 0.004 0.055 2606 Dihedral : 3.484 15.765 2117 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.31 % Allowed : 11.56 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1976 helix: 2.13 (0.15), residues: 1312 sheet: -3.29 (0.69), residues: 45 loop : -1.00 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 406 TYR 0.020 0.001 TYR F 128 PHE 0.027 0.001 PHE C 402 TRP 0.008 0.001 TRP F 127 HIS 0.003 0.001 HIS S 64 Details of bonding type rmsd covalent geometry : bond 0.00249 (14995) covalent geometry : angle 0.48436 (20362) hydrogen bonds : bond 0.03828 ( 925) hydrogen bonds : angle 3.72985 ( 2742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 318 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: C 121 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6910 (mt0) REVERT: C 186 LEU cc_start: 0.7998 (tp) cc_final: 0.7769 (tp) REVERT: C 251 PHE cc_start: 0.7961 (t80) cc_final: 0.7640 (t80) REVERT: C 285 ASP cc_start: 0.7549 (p0) cc_final: 0.7328 (p0) REVERT: C 301 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: C 302 ILE cc_start: 0.8537 (tt) cc_final: 0.8288 (pt) REVERT: C 706 ASP cc_start: 0.6938 (m-30) cc_final: 0.6671 (m-30) REVERT: C 724 VAL cc_start: 0.7798 (t) cc_final: 0.7539 (p) REVERT: C 743 LYS cc_start: 0.8130 (mttp) cc_final: 0.7820 (ttmm) REVERT: D 33 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: D 51 LYS cc_start: 0.7145 (tptp) cc_final: 0.6664 (tptp) REVERT: D 221 GLU cc_start: 0.6627 (tp30) cc_final: 0.6386 (tp30) REVERT: D 234 TYR cc_start: 0.8149 (m-80) cc_final: 0.7885 (m-80) REVERT: D 444 LYS cc_start: 0.8056 (mttm) cc_final: 0.7780 (mtpp) REVERT: D 446 LYS cc_start: 0.8166 (mppt) cc_final: 0.7859 (mppt) REVERT: D 518 GLN cc_start: 0.7672 (tp40) cc_final: 0.7181 (tp40) REVERT: D 624 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7609 (p) REVERT: D 690 ILE cc_start: 0.8099 (tp) cc_final: 0.7777 (tt) REVERT: D 713 ILE cc_start: 0.8040 (mm) cc_final: 0.7803 (mt) REVERT: D 793 LYS cc_start: 0.7430 (mtmt) cc_final: 0.6739 (mtmt) REVERT: D 797 TYR cc_start: 0.6468 (m-80) cc_final: 0.6262 (m-80) REVERT: F 117 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7323 (pt) REVERT: S 57 LYS cc_start: 0.7907 (mppt) cc_final: 0.7606 (mmtm) outliers start: 19 outliers final: 9 residues processed: 325 average time/residue: 0.1245 time to fit residues: 58.0930 Evaluate side-chains 318 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 304 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 146 optimal weight: 0.0980 chunk 181 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN D 442 GLN D 463 ASN ** S 108 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.150198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121880 restraints weight = 24594.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125233 restraints weight = 11727.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127406 restraints weight = 6908.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128597 restraints weight = 4716.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129569 restraints weight = 3688.734| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14995 Z= 0.119 Angle : 0.483 6.630 20362 Z= 0.255 Chirality : 0.038 0.141 2465 Planarity : 0.004 0.051 2606 Dihedral : 3.479 16.317 2117 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.79 % Allowed : 13.08 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1976 helix: 2.16 (0.15), residues: 1312 sheet: -2.98 (0.67), residues: 49 loop : -1.05 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 285 TYR 0.019 0.001 TYR C 278 PHE 0.025 0.001 PHE C 402 TRP 0.009 0.001 TRP S 88 HIS 0.003 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00271 (14995) covalent geometry : angle 0.48331 (20362) hydrogen bonds : bond 0.03939 ( 925) hydrogen bonds : angle 3.64988 ( 2742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 314 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: C 95 PHE cc_start: 0.8232 (t80) cc_final: 0.7782 (t80) REVERT: C 121 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6683 (mt0) REVERT: C 251 PHE cc_start: 0.7984 (t80) cc_final: 0.7699 (t80) REVERT: C 285 ASP cc_start: 0.7572 (p0) cc_final: 0.7357 (p0) REVERT: C 301 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: C 706 ASP cc_start: 0.6947 (m-30) cc_final: 0.6696 (m-30) REVERT: C 743 LYS cc_start: 0.8139 (mttp) cc_final: 0.7818 (ttmm) REVERT: C 756 LEU cc_start: 0.7779 (mt) cc_final: 0.7575 (mt) REVERT: D 30 LEU cc_start: 0.8367 (tt) cc_final: 0.8010 (tt) REVERT: D 33 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5757 (mp0) REVERT: D 221 GLU cc_start: 0.6721 (tp30) cc_final: 0.6446 (tp30) REVERT: D 234 TYR cc_start: 0.8119 (m-80) cc_final: 0.7867 (m-80) REVERT: D 444 LYS cc_start: 0.8118 (mttm) cc_final: 0.7829 (mtpp) REVERT: D 446 LYS cc_start: 0.8167 (mppt) cc_final: 0.7869 (mppt) REVERT: D 518 GLN cc_start: 0.7690 (tp40) cc_final: 0.7221 (tp40) REVERT: D 624 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7634 (p) REVERT: D 793 LYS cc_start: 0.7444 (mtmt) cc_final: 0.6834 (mtmt) REVERT: D 797 TYR cc_start: 0.6454 (m-80) cc_final: 0.6223 (m-80) REVERT: F 117 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7376 (pt) REVERT: S 57 LYS cc_start: 0.7921 (mppt) cc_final: 0.7627 (mmtm) REVERT: S 88 TRP cc_start: 0.6319 (t-100) cc_final: 0.5884 (t-100) outliers start: 26 outliers final: 12 residues processed: 324 average time/residue: 0.1215 time to fit residues: 56.7774 Evaluate side-chains 319 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 302 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 157 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 146 optimal weight: 0.0270 chunk 153 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 63 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN C 386 ASN S 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.151752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123935 restraints weight = 24575.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127211 restraints weight = 11722.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129335 restraints weight = 6917.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130692 restraints weight = 4721.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131635 restraints weight = 3617.408| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14995 Z= 0.104 Angle : 0.481 8.222 20362 Z= 0.251 Chirality : 0.037 0.136 2465 Planarity : 0.004 0.048 2606 Dihedral : 3.386 17.358 2117 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.93 % Allowed : 13.90 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.20), residues: 1976 helix: 2.21 (0.15), residues: 1316 sheet: -3.04 (0.67), residues: 49 loop : -1.00 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 285 TYR 0.018 0.001 TYR C 278 PHE 0.029 0.001 PHE C 569 TRP 0.008 0.001 TRP S 88 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00228 (14995) covalent geometry : angle 0.48107 (20362) hydrogen bonds : bond 0.03448 ( 925) hydrogen bonds : angle 3.53970 ( 2742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 0.505 Fit side-chains REVERT: C 95 PHE cc_start: 0.8186 (t80) cc_final: 0.7746 (t80) REVERT: C 121 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6775 (mt0) REVERT: C 186 LEU cc_start: 0.7976 (tp) cc_final: 0.7746 (tp) REVERT: C 251 PHE cc_start: 0.7944 (t80) cc_final: 0.7703 (t80) REVERT: C 285 ASP cc_start: 0.7558 (p0) cc_final: 0.7352 (p0) REVERT: C 301 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: C 706 ASP cc_start: 0.6906 (m-30) cc_final: 0.6627 (m-30) REVERT: C 756 LEU cc_start: 0.7789 (mt) cc_final: 0.7578 (mt) REVERT: D 30 LEU cc_start: 0.8371 (tt) cc_final: 0.8046 (tt) REVERT: D 33 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5747 (mp0) REVERT: D 51 LYS cc_start: 0.7202 (tptp) cc_final: 0.6714 (tptp) REVERT: D 221 GLU cc_start: 0.6734 (tp30) cc_final: 0.6417 (tp30) REVERT: D 234 TYR cc_start: 0.8067 (m-80) cc_final: 0.7764 (m-80) REVERT: D 281 SER cc_start: 0.8595 (m) cc_final: 0.7979 (p) REVERT: D 444 LYS cc_start: 0.8031 (mttm) cc_final: 0.7720 (mtpp) REVERT: D 446 LYS cc_start: 0.8170 (mppt) cc_final: 0.7860 (mppt) REVERT: D 518 GLN cc_start: 0.7672 (tp40) cc_final: 0.7205 (tp40) REVERT: D 538 GLU cc_start: 0.7799 (tp30) cc_final: 0.7282 (mm-30) REVERT: D 614 ILE cc_start: 0.8306 (mm) cc_final: 0.8063 (tp) REVERT: D 624 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7592 (p) REVERT: D 793 LYS cc_start: 0.7493 (mtmt) cc_final: 0.6919 (mtmt) REVERT: D 797 TYR cc_start: 0.6430 (m-80) cc_final: 0.6221 (m-80) REVERT: S 57 LYS cc_start: 0.7934 (mppt) cc_final: 0.7708 (mmtm) REVERT: S 88 TRP cc_start: 0.6268 (t-100) cc_final: 0.5818 (t-100) outliers start: 28 outliers final: 15 residues processed: 321 average time/residue: 0.1203 time to fit residues: 56.2297 Evaluate side-chains 322 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 95 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 ASN ** S 64 HIS ** 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 = 0.3920 r_free = 0.3920 target = 0.147758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119227 restraints weight = 24600.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122388 restraints weight = 11841.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124554 restraints weight = 7232.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125927 restraints weight = 4978.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126861 restraints weight = 3831.009| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14995 Z= 0.158 Angle : 0.535 10.185 20362 Z= 0.277 Chirality : 0.040 0.146 2465 Planarity : 0.004 0.046 2606 Dihedral : 3.580 21.229 2117 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.65 % Allowed : 14.80 % Favored : 83.55 % 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: 1.60 (0.20), residues: 1976 helix: 2.11 (0.15), residues: 1312 sheet: -2.76 (0.77), residues: 40 loop : -1.00 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 506 TYR 0.021 0.001 TYR C 278 PHE 0.023 0.001 PHE C 402 TRP 0.010 0.001 TRP S 88 HIS 0.005 0.001 HIS S 64 Details of bonding type rmsd covalent geometry : bond 0.00370 (14995) covalent geometry : angle 0.53480 (20362) hydrogen bonds : bond 0.04601 ( 925) hydrogen bonds : angle 3.72243 ( 2742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 319 time to evaluate : 0.353 Fit side-chains REVERT: C 95 PHE cc_start: 0.8235 (t80) cc_final: 0.7776 (t80) REVERT: C 121 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: C 185 LYS cc_start: 0.7644 (mmmm) cc_final: 0.7426 (mmmm) REVERT: C 210 GLU cc_start: 0.7804 (tp30) cc_final: 0.7491 (tp30) REVERT: C 251 PHE cc_start: 0.8031 (t80) cc_final: 0.7778 (t80) REVERT: C 301 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: C 472 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7962 (mptt) REVERT: C 663 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6868 (mp) REVERT: C 706 ASP cc_start: 0.6935 (m-30) cc_final: 0.6715 (m-30) REVERT: C 743 LYS cc_start: 0.8129 (mttp) cc_final: 0.7801 (ttmm) REVERT: D 30 LEU cc_start: 0.8367 (tt) cc_final: 0.8043 (tt) REVERT: D 33 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5882 (mp0) REVERT: D 221 GLU cc_start: 0.6776 (tp30) cc_final: 0.6450 (tp30) REVERT: D 274 TYR cc_start: 0.7904 (m-80) cc_final: 0.7453 (m-80) REVERT: D 281 SER cc_start: 0.8620 (m) cc_final: 0.8037 (p) REVERT: D 444 LYS cc_start: 0.8132 (mttm) cc_final: 0.7801 (mtpp) REVERT: D 446 LYS cc_start: 0.8192 (mppt) cc_final: 0.7852 (mppt) REVERT: D 518 GLN cc_start: 0.7696 (tp40) cc_final: 0.7306 (tp40) REVERT: D 538 GLU cc_start: 0.7955 (tp30) cc_final: 0.7297 (mm-30) REVERT: D 564 TYR cc_start: 0.8201 (m-80) cc_final: 0.7781 (m-80) REVERT: D 624 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7599 (p) REVERT: D 793 LYS cc_start: 0.7516 (mtmt) cc_final: 0.7030 (mtmt) REVERT: D 797 TYR cc_start: 0.6502 (m-80) cc_final: 0.6249 (m-80) REVERT: D 840 LEU cc_start: 0.7712 (mt) cc_final: 0.7442 (mt) REVERT: S 57 LYS cc_start: 0.7979 (mppt) cc_final: 0.7678 (mmtm) REVERT: S 88 TRP cc_start: 0.6335 (t-100) cc_final: 0.5927 (t-100) outliers start: 24 outliers final: 15 residues processed: 328 average time/residue: 0.1225 time to fit residues: 57.6594 Evaluate side-chains 335 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 40 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN C 386 ASN ** S 64 HIS ** 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 = 0.3928 r_free = 0.3928 target = 0.148608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120683 restraints weight = 24525.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123940 restraints weight = 11757.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126028 restraints weight = 6926.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127414 restraints weight = 4735.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128235 restraints weight = 3649.292| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14995 Z= 0.149 Angle : 0.532 12.199 20362 Z= 0.276 Chirality : 0.040 0.155 2465 Planarity : 0.004 0.045 2606 Dihedral : 3.605 21.450 2117 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 15.97 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 1976 helix: 2.08 (0.15), residues: 1311 sheet: -2.79 (0.78), residues: 40 loop : -1.03 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 285 TYR 0.021 0.001 TYR C 278 PHE 0.029 0.001 PHE C 569 TRP 0.009 0.001 TRP S 88 HIS 0.005 0.001 HIS S 64 Details of bonding type rmsd covalent geometry : bond 0.00349 (14995) covalent geometry : angle 0.53194 (20362) hydrogen bonds : bond 0.04430 ( 925) hydrogen bonds : angle 3.75097 ( 2742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 317 time to evaluate : 0.535 Fit side-chains REVERT: C 95 PHE cc_start: 0.8190 (t80) cc_final: 0.7726 (t80) REVERT: C 121 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: C 185 LYS cc_start: 0.7655 (mmmm) cc_final: 0.7438 (mmmm) REVERT: C 210 GLU cc_start: 0.7788 (tp30) cc_final: 0.7499 (tp30) REVERT: C 251 PHE cc_start: 0.8025 (t80) cc_final: 0.7798 (t80) REVERT: C 301 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: C 706 ASP cc_start: 0.6946 (m-30) cc_final: 0.6708 (m-30) REVERT: C 743 LYS cc_start: 0.8099 (mttp) cc_final: 0.7803 (ttmm) REVERT: D 30 LEU cc_start: 0.8371 (tt) cc_final: 0.8059 (tt) REVERT: D 33 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: D 221 GLU cc_start: 0.6813 (tp30) cc_final: 0.6511 (tp30) REVERT: D 274 TYR cc_start: 0.7870 (m-80) cc_final: 0.7375 (m-80) REVERT: D 281 SER cc_start: 0.8596 (m) cc_final: 0.8019 (p) REVERT: D 444 LYS cc_start: 0.8119 (mttm) cc_final: 0.7800 (mtpp) REVERT: D 446 LYS cc_start: 0.8183 (mppt) cc_final: 0.7853 (mppt) REVERT: D 518 GLN cc_start: 0.7721 (tp40) cc_final: 0.7337 (tp40) REVERT: D 564 TYR cc_start: 0.8194 (m-80) cc_final: 0.7814 (m-80) REVERT: D 624 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7482 (p) REVERT: D 793 LYS cc_start: 0.7536 (mtmt) cc_final: 0.7107 (mtmt) REVERT: D 797 TYR cc_start: 0.6453 (m-80) cc_final: 0.6248 (m-80) REVERT: D 840 LEU cc_start: 0.7678 (mt) cc_final: 0.7390 (mt) REVERT: S 57 LYS cc_start: 0.7977 (mppt) cc_final: 0.7666 (mmtm) REVERT: S 88 TRP cc_start: 0.6316 (t-100) cc_final: 0.6042 (t-100) outliers start: 27 outliers final: 16 residues processed: 329 average time/residue: 0.1240 time to fit residues: 58.5637 Evaluate side-chains 334 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 314 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 47 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120823 restraints weight = 24696.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124304 restraints weight = 11481.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126520 restraints weight = 6639.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128018 restraints weight = 4477.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128656 restraints weight = 3380.666| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14995 Z= 0.136 Angle : 0.538 12.212 20362 Z= 0.277 Chirality : 0.039 0.154 2465 Planarity : 0.004 0.043 2606 Dihedral : 3.576 21.432 2117 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.72 % Allowed : 16.72 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.20), residues: 1976 helix: 2.10 (0.15), residues: 1311 sheet: -2.81 (0.79), residues: 40 loop : -1.01 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 285 TYR 0.021 0.001 TYR C 278 PHE 0.022 0.001 PHE C 402 TRP 0.008 0.001 TRP F 127 HIS 0.003 0.001 HIS S 64 Details of bonding type rmsd covalent geometry : bond 0.00318 (14995) covalent geometry : angle 0.53788 (20362) hydrogen bonds : bond 0.04224 ( 925) hydrogen bonds : angle 3.71011 ( 2742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 314 time to evaluate : 0.525 Fit side-chains REVERT: C 95 PHE cc_start: 0.8184 (t80) cc_final: 0.7702 (t80) REVERT: C 121 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6867 (mt0) REVERT: C 185 LYS cc_start: 0.7657 (mmmm) cc_final: 0.7441 (mmmm) REVERT: C 210 GLU cc_start: 0.7784 (tp30) cc_final: 0.7510 (tp30) REVERT: C 251 PHE cc_start: 0.8012 (t80) cc_final: 0.7788 (t80) REVERT: C 301 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: C 706 ASP cc_start: 0.6928 (m-30) cc_final: 0.6695 (m-30) REVERT: C 743 LYS cc_start: 0.8093 (mttp) cc_final: 0.7798 (ttmm) REVERT: D 30 LEU cc_start: 0.8384 (tt) cc_final: 0.8093 (tt) REVERT: D 33 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5896 (mp0) REVERT: D 221 GLU cc_start: 0.6760 (tp30) cc_final: 0.6521 (tp30) REVERT: D 274 TYR cc_start: 0.7861 (m-80) cc_final: 0.7362 (m-80) REVERT: D 281 SER cc_start: 0.8584 (m) cc_final: 0.7986 (p) REVERT: D 344 ASP cc_start: 0.7626 (t0) cc_final: 0.7422 (t0) REVERT: D 444 LYS cc_start: 0.8113 (mttm) cc_final: 0.7792 (mtpp) REVERT: D 446 LYS cc_start: 0.8186 (mppt) cc_final: 0.7850 (mppt) REVERT: D 518 GLN cc_start: 0.7708 (tp40) cc_final: 0.7366 (tp40) REVERT: D 564 TYR cc_start: 0.8189 (m-80) cc_final: 0.7850 (m-80) REVERT: D 624 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7581 (p) REVERT: D 690 ILE cc_start: 0.8135 (tp) cc_final: 0.7879 (tt) REVERT: D 793 LYS cc_start: 0.7508 (mtmt) cc_final: 0.7123 (mtmt) REVERT: D 840 LEU cc_start: 0.7681 (mt) cc_final: 0.7383 (mt) REVERT: S 57 LYS cc_start: 0.7967 (mppt) cc_final: 0.7705 (mmtm) outliers start: 25 outliers final: 16 residues processed: 324 average time/residue: 0.1238 time to fit residues: 57.6616 Evaluate side-chains 332 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 312 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 759 LYS Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 95 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN C 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.149072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121014 restraints weight = 24576.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124296 restraints weight = 11808.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126530 restraints weight = 6983.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127787 restraints weight = 4740.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128775 restraints weight = 3679.277| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14995 Z= 0.121 Angle : 0.536 12.358 20362 Z= 0.275 Chirality : 0.039 0.175 2465 Planarity : 0.004 0.043 2606 Dihedral : 3.520 21.331 2117 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.45 % Allowed : 17.48 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.20), residues: 1976 helix: 2.18 (0.15), residues: 1305 sheet: -2.85 (0.79), residues: 40 loop : -1.00 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 506 TYR 0.033 0.001 TYR D 797 PHE 0.020 0.001 PHE C 402 TRP 0.007 0.001 TRP R 33 HIS 0.003 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00276 (14995) covalent geometry : angle 0.53645 (20362) hydrogen bonds : bond 0.03934 ( 925) hydrogen bonds : angle 3.66488 ( 2742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 313 time to evaluate : 0.552 Fit side-chains REVERT: C 95 PHE cc_start: 0.8165 (t80) cc_final: 0.7662 (t80) REVERT: C 121 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6707 (mt0) REVERT: C 185 LYS cc_start: 0.7649 (mmmm) cc_final: 0.7422 (mmmm) REVERT: C 210 GLU cc_start: 0.7795 (tp30) cc_final: 0.7523 (tp30) REVERT: C 251 PHE cc_start: 0.8001 (t80) cc_final: 0.7779 (t80) REVERT: C 301 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: C 458 ASP cc_start: 0.7717 (m-30) cc_final: 0.6994 (m-30) REVERT: C 706 ASP cc_start: 0.6933 (m-30) cc_final: 0.6660 (m-30) REVERT: D 30 LEU cc_start: 0.8379 (tt) cc_final: 0.8076 (tt) REVERT: D 33 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5869 (mp0) REVERT: D 221 GLU cc_start: 0.6733 (tp30) cc_final: 0.6504 (tp30) REVERT: D 234 TYR cc_start: 0.8119 (m-80) cc_final: 0.7815 (m-80) REVERT: D 281 SER cc_start: 0.8586 (m) cc_final: 0.7989 (p) REVERT: D 444 LYS cc_start: 0.8063 (mttm) cc_final: 0.7745 (mtpp) REVERT: D 446 LYS cc_start: 0.8192 (mppt) cc_final: 0.7854 (mppt) REVERT: D 518 GLN cc_start: 0.7669 (tp40) cc_final: 0.7358 (tp40) REVERT: D 564 TYR cc_start: 0.8172 (m-80) cc_final: 0.7886 (m-80) REVERT: D 624 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7542 (p) REVERT: D 690 ILE cc_start: 0.8110 (tp) cc_final: 0.7856 (tt) REVERT: D 840 LEU cc_start: 0.7660 (mt) cc_final: 0.7369 (mt) REVERT: S 57 LYS cc_start: 0.7959 (mppt) cc_final: 0.7706 (mmtm) outliers start: 21 outliers final: 14 residues processed: 321 average time/residue: 0.1221 time to fit residues: 56.5982 Evaluate side-chains 327 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 309 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.149421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121167 restraints weight = 24491.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124657 restraints weight = 11281.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126908 restraints weight = 6532.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128264 restraints weight = 4394.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129196 restraints weight = 3385.591| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14995 Z= 0.133 Angle : 0.550 12.410 20362 Z= 0.282 Chirality : 0.039 0.166 2465 Planarity : 0.004 0.044 2606 Dihedral : 3.542 21.232 2117 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.51 % Allowed : 17.48 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.20), residues: 1976 helix: 2.15 (0.15), residues: 1306 sheet: -2.81 (0.81), residues: 40 loop : -0.96 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 506 TYR 0.038 0.001 TYR D 797 PHE 0.021 0.001 PHE C 402 TRP 0.008 0.001 TRP F 127 HIS 0.003 0.001 HIS S 64 Details of bonding type rmsd covalent geometry : bond 0.00308 (14995) covalent geometry : angle 0.54986 (20362) hydrogen bonds : bond 0.04130 ( 925) hydrogen bonds : angle 3.70804 ( 2742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 312 time to evaluate : 0.542 Fit side-chains REVERT: C 95 PHE cc_start: 0.8155 (t80) cc_final: 0.7671 (t80) REVERT: C 97 LYS cc_start: 0.8256 (tppt) cc_final: 0.7857 (tppt) REVERT: C 121 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6769 (mt0) REVERT: C 185 LYS cc_start: 0.7654 (mmmm) cc_final: 0.7435 (mmmm) REVERT: C 251 PHE cc_start: 0.8030 (t80) cc_final: 0.7800 (t80) REVERT: C 396 ASP cc_start: 0.6962 (m-30) cc_final: 0.6580 (m-30) REVERT: C 694 GLN cc_start: 0.7846 (tp40) cc_final: 0.7524 (tp40) REVERT: C 706 ASP cc_start: 0.6919 (m-30) cc_final: 0.6679 (m-30) REVERT: D 30 LEU cc_start: 0.8378 (tt) cc_final: 0.8076 (tt) REVERT: D 33 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5876 (mp0) REVERT: D 281 SER cc_start: 0.8586 (m) cc_final: 0.7985 (p) REVERT: D 344 ASP cc_start: 0.7632 (t0) cc_final: 0.7429 (t0) REVERT: D 444 LYS cc_start: 0.8097 (mttm) cc_final: 0.7777 (mtpp) REVERT: D 446 LYS cc_start: 0.8193 (mppt) cc_final: 0.7854 (mppt) REVERT: D 460 GLU cc_start: 0.7824 (tp30) cc_final: 0.7572 (tp30) REVERT: D 518 GLN cc_start: 0.7670 (tp40) cc_final: 0.7315 (tp40) REVERT: D 564 TYR cc_start: 0.8172 (m-80) cc_final: 0.7829 (m-80) REVERT: D 624 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7569 (p) REVERT: D 690 ILE cc_start: 0.8128 (tp) cc_final: 0.7879 (tt) REVERT: D 840 LEU cc_start: 0.7673 (mt) cc_final: 0.7382 (mt) REVERT: S 57 LYS cc_start: 0.7958 (mppt) cc_final: 0.7701 (mmtm) outliers start: 22 outliers final: 15 residues processed: 320 average time/residue: 0.1178 time to fit residues: 54.4757 Evaluate side-chains 328 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 175 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.149220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121224 restraints weight = 24321.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124537 restraints weight = 11605.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126708 restraints weight = 6854.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128112 restraints weight = 4677.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128847 restraints weight = 3577.222| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14995 Z= 0.127 Angle : 0.550 12.557 20362 Z= 0.284 Chirality : 0.039 0.158 2465 Planarity : 0.004 0.044 2606 Dihedral : 3.509 20.842 2117 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.31 % Allowed : 18.17 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.20), residues: 1976 helix: 2.16 (0.15), residues: 1307 sheet: -2.63 (0.79), residues: 42 loop : -0.92 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 285 TYR 0.048 0.001 TYR D 797 PHE 0.021 0.001 PHE C 402 TRP 0.007 0.001 TRP D 347 HIS 0.003 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00294 (14995) covalent geometry : angle 0.55011 (20362) hydrogen bonds : bond 0.03998 ( 925) hydrogen bonds : angle 3.68880 ( 2742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.58 seconds wall clock time: 47 minutes 31.05 seconds (2851.05 seconds total)