Starting phenix.real_space_refine on Fri Sep 27 01:57:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbw_14594/09_2024/7zbw_14594.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbw_14594/09_2024/7zbw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbw_14594/09_2024/7zbw_14594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbw_14594/09_2024/7zbw_14594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbw_14594/09_2024/7zbw_14594.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbw_14594/09_2024/7zbw_14594.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'TYR:plan': 2, 'ARG: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: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} 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: {'GLN:plan1': 15, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 12, 'GLU:plan': 14, 'ARG:plan': 13} 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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 8.70, per 1000 atoms: 0.59 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: 3.69 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.86 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: 4.64 Time building geometry restraints manager: 4.31 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: 1.990 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.030 ------------------------------------------------------------------------------- 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= 0.195 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.023 0.001 TRP S 61 HIS 0.005 0.001 HIS C 345 PHE 0.019 0.001 PHE C 402 TYR 0.018 0.001 TYR C 278 ARG 0.004 0.000 ARG C 506 *********************** 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 fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 1.589 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: 0.7391 (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: 0.6784 (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: 0.2936 time to fit residues: 140.7390 Evaluate side-chains 314 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 0.0010 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 180 optimal weight: 20.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14995 Z= 0.182 Angle : 0.511 7.136 20362 Z= 0.270 Chirality : 0.038 0.153 2465 Planarity : 0.004 0.064 2606 Dihedral : 3.638 16.616 2117 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.89 % Allowed : 9.08 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 1976 helix: 2.02 (0.15), residues: 1313 sheet: -3.15 (0.73), residues: 44 loop : -1.21 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 61 HIS 0.004 0.001 HIS C 345 PHE 0.031 0.001 PHE C 402 TYR 0.021 0.001 TYR C 278 ARG 0.003 0.000 ARG D 406 *********************** 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 334 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 321 time to evaluate : 1.638 Fit side-chains REVERT: C 121 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6967 (mt0) REVERT: C 154 LYS cc_start: 0.7775 (mmpt) cc_final: 0.7572 (mmtm) REVERT: C 225 LEU cc_start: 0.8285 (mt) cc_final: 0.8066 (mt) REVERT: C 285 ASP cc_start: 0.7650 (p0) cc_final: 0.7357 (p0) REVERT: C 301 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: C 302 ILE cc_start: 0.8575 (tt) cc_final: 0.8300 (pt) REVERT: C 706 ASP cc_start: 0.6943 (m-30) cc_final: 0.6697 (m-30) REVERT: C 724 VAL cc_start: 0.7939 (t) cc_final: 0.7681 (p) REVERT: D 51 LYS cc_start: 0.7241 (tptp) cc_final: 0.6730 (tptp) REVERT: D 221 GLU cc_start: 0.6774 (tp30) cc_final: 0.6534 (tp30) REVERT: D 274 TYR cc_start: 0.7848 (m-80) cc_final: 0.7569 (m-80) REVERT: D 444 LYS cc_start: 0.8070 (mttm) cc_final: 0.7815 (mtpp) REVERT: D 446 LYS cc_start: 0.8154 (mppt) cc_final: 0.7842 (mppt) REVERT: D 518 GLN cc_start: 0.7662 (tp40) cc_final: 0.7178 (tp40) REVERT: D 703 GLU cc_start: 0.7363 (pp20) cc_final: 0.6917 (pp20) REVERT: D 729 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7840 (mmmm) REVERT: D 737 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6893 (mm-30) REVERT: D 793 LYS cc_start: 0.7853 (mtmt) cc_final: 0.6981 (mtmt) REVERT: D 797 TYR cc_start: 0.6862 (m-80) cc_final: 0.6318 (m-80) REVERT: F 127 TRP cc_start: 0.7986 (m-10) cc_final: 0.7705 (m-10) outliers start: 13 outliers final: 5 residues processed: 324 average time/residue: 0.2823 time to fit residues: 130.9884 Evaluate side-chains 307 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 300 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 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 100 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 150 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 179 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS D 442 GLN D 463 ASN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14995 Z= 0.309 Angle : 0.555 7.511 20362 Z= 0.295 Chirality : 0.041 0.160 2465 Planarity : 0.004 0.058 2606 Dihedral : 3.918 19.458 2117 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.79 % Allowed : 12.32 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1976 helix: 1.80 (0.14), residues: 1307 sheet: -2.98 (0.80), residues: 35 loop : -1.12 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 137 HIS 0.005 0.001 HIS C 476 PHE 0.028 0.002 PHE C 402 TYR 0.023 0.002 TYR C 278 ARG 0.005 0.000 ARG D 406 *********************** 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 354 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 328 time to evaluate : 1.604 Fit side-chains REVERT: C 95 PHE cc_start: 0.8251 (t80) cc_final: 0.7782 (t80) REVERT: C 301 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 537 ILE cc_start: 0.8354 (tp) cc_final: 0.8063 (tp) REVERT: C 712 GLN cc_start: 0.7706 (tt0) cc_final: 0.7488 (tt0) REVERT: C 743 LYS cc_start: 0.8097 (mttp) cc_final: 0.7683 (ttmm) REVERT: D 33 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: D 221 GLU cc_start: 0.6832 (tp30) cc_final: 0.6595 (tp30) REVERT: D 274 TYR cc_start: 0.7927 (m-80) cc_final: 0.7608 (m-80) REVERT: D 444 LYS cc_start: 0.8160 (mttm) cc_final: 0.7858 (mtpp) REVERT: D 446 LYS cc_start: 0.8167 (mppt) cc_final: 0.7824 (mppt) REVERT: D 481 ILE cc_start: 0.8199 (mt) cc_final: 0.7981 (mp) REVERT: D 518 GLN cc_start: 0.7720 (tp40) cc_final: 0.7240 (tp40) REVERT: D 538 GLU cc_start: 0.7930 (tp30) cc_final: 0.7367 (tp30) REVERT: D 624 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7627 (p) REVERT: D 737 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6876 (mm-30) REVERT: D 793 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7186 (mtmt) REVERT: D 797 TYR cc_start: 0.6877 (m-80) cc_final: 0.6402 (m-80) REVERT: D 840 LEU cc_start: 0.7749 (mt) cc_final: 0.7474 (mt) REVERT: F 117 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7483 (pt) REVERT: S 57 LYS cc_start: 0.7965 (mppt) cc_final: 0.7642 (mmtm) outliers start: 26 outliers final: 13 residues processed: 335 average time/residue: 0.2860 time to fit residues: 136.4769 Evaluate side-chains 328 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 311 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 759 LYS Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 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 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 117 LEU Chi-restraints excluded: chain F residue 135 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 50.0000 chunk 136 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 181 optimal weight: 40.0000 chunk 192 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 172 optimal weight: 9.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14995 Z= 0.170 Angle : 0.498 7.821 20362 Z= 0.262 Chirality : 0.038 0.142 2465 Planarity : 0.004 0.053 2606 Dihedral : 3.659 17.705 2117 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.93 % Allowed : 14.25 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 1976 helix: 2.02 (0.15), residues: 1309 sheet: -3.11 (0.77), residues: 35 loop : -1.10 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 33 HIS 0.004 0.001 HIS C 345 PHE 0.026 0.001 PHE C 569 TYR 0.022 0.001 TYR F 128 ARG 0.006 0.000 ARG D 285 *********************** 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 349 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 321 time to evaluate : 1.628 Fit side-chains REVERT: C 95 PHE cc_start: 0.8186 (t80) cc_final: 0.7753 (t80) REVERT: C 154 LYS cc_start: 0.7903 (mmpt) cc_final: 0.7651 (mmtm) REVERT: C 251 PHE cc_start: 0.8044 (t80) cc_final: 0.7752 (t80) REVERT: C 301 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: C 357 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7432 (mm-30) REVERT: C 436 ASN cc_start: 0.7910 (t0) cc_final: 0.7695 (t0) REVERT: C 537 ILE cc_start: 0.8367 (tp) cc_final: 0.8055 (tp) REVERT: C 663 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6741 (mp) REVERT: C 743 LYS cc_start: 0.8082 (mttp) cc_final: 0.7804 (ttmm) REVERT: D 30 LEU cc_start: 0.8242 (tt) cc_final: 0.7948 (tt) REVERT: D 33 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5900 (mp0) REVERT: D 185 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7897 (t) REVERT: D 274 TYR cc_start: 0.7843 (m-80) cc_final: 0.7465 (m-80) REVERT: D 281 SER cc_start: 0.8532 (m) cc_final: 0.7954 (p) REVERT: D 444 LYS cc_start: 0.8082 (mttm) cc_final: 0.7780 (mtpp) REVERT: D 446 LYS cc_start: 0.8162 (mppt) cc_final: 0.7850 (mppt) REVERT: D 481 ILE cc_start: 0.8202 (mt) cc_final: 0.7993 (mp) REVERT: D 518 GLN cc_start: 0.7727 (tp40) cc_final: 0.7283 (tp40) REVERT: D 624 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7449 (p) REVERT: D 737 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6888 (mm-30) REVERT: D 793 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7111 (mtmt) REVERT: D 797 TYR cc_start: 0.6829 (m-80) cc_final: 0.6357 (m-80) REVERT: S 57 LYS cc_start: 0.7991 (mppt) cc_final: 0.7658 (mmtm) outliers start: 28 outliers final: 14 residues processed: 330 average time/residue: 0.2714 time to fit residues: 129.6448 Evaluate side-chains 327 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 308 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 301 GLU 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 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 185 THR Chi-restraints excluded: chain D residue 256 ILE 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 Chi-restraints excluded: chain F residue 135 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.0970 chunk 172 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14995 Z= 0.195 Angle : 0.515 10.369 20362 Z= 0.268 Chirality : 0.038 0.150 2465 Planarity : 0.004 0.049 2606 Dihedral : 3.648 20.675 2117 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.72 % Allowed : 15.62 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 1976 helix: 2.04 (0.15), residues: 1309 sheet: -2.83 (0.76), residues: 40 loop : -1.05 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 88 HIS 0.005 0.001 HIS S 64 PHE 0.027 0.001 PHE C 569 TYR 0.024 0.001 TYR F 128 ARG 0.005 0.000 ARG D 285 *********************** 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 343 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 318 time to evaluate : 1.726 Fit side-chains REVERT: C 95 PHE cc_start: 0.8200 (t80) cc_final: 0.7765 (t80) REVERT: C 185 LYS cc_start: 0.7638 (mmmm) cc_final: 0.7396 (mmmm) REVERT: C 251 PHE cc_start: 0.8051 (t80) cc_final: 0.7814 (t80) REVERT: C 301 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: C 537 ILE cc_start: 0.8368 (tp) cc_final: 0.8043 (tp) REVERT: C 663 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6737 (mp) REVERT: C 743 LYS cc_start: 0.8111 (mttp) cc_final: 0.7812 (ttmm) REVERT: D 30 LEU cc_start: 0.8248 (tt) cc_final: 0.7959 (tt) REVERT: D 33 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: D 185 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7914 (t) REVERT: D 234 TYR cc_start: 0.8151 (m-80) cc_final: 0.7871 (m-80) REVERT: D 274 TYR cc_start: 0.7840 (m-80) cc_final: 0.7485 (m-80) REVERT: D 281 SER cc_start: 0.8543 (m) cc_final: 0.7963 (p) REVERT: D 444 LYS cc_start: 0.8126 (mttm) cc_final: 0.7796 (mtpp) REVERT: D 446 LYS cc_start: 0.8171 (mppt) cc_final: 0.7847 (mppt) REVERT: D 518 GLN cc_start: 0.7708 (tp40) cc_final: 0.7235 (tp40) REVERT: D 538 GLU cc_start: 0.7928 (tp30) cc_final: 0.7260 (mm-30) REVERT: D 624 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7528 (p) REVERT: D 737 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6901 (mm-30) REVERT: D 793 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7212 (mtmt) REVERT: D 797 TYR cc_start: 0.6830 (m-80) cc_final: 0.6365 (m-80) REVERT: D 840 LEU cc_start: 0.7734 (mt) cc_final: 0.7426 (mt) REVERT: S 57 LYS cc_start: 0.8017 (mppt) cc_final: 0.7693 (mmtm) outliers start: 25 outliers final: 15 residues processed: 328 average time/residue: 0.2572 time to fit residues: 120.9790 Evaluate side-chains 334 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 314 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 663 LEU Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain C residue 709 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 185 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1604 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= 0.191 Angle : 0.523 11.355 20362 Z= 0.270 Chirality : 0.039 0.150 2465 Planarity : 0.004 0.046 2606 Dihedral : 3.603 20.979 2117 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.00 % Allowed : 16.10 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 1976 helix: 2.07 (0.15), residues: 1309 sheet: -2.94 (0.75), residues: 40 loop : -1.04 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 88 HIS 0.006 0.001 HIS S 64 PHE 0.028 0.001 PHE C 569 TYR 0.024 0.001 TYR F 128 ARG 0.006 0.000 ARG D 285 *********************** 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 338 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 309 time to evaluate : 1.609 Fit side-chains REVERT: C 95 PHE cc_start: 0.8167 (t80) cc_final: 0.7725 (t80) REVERT: C 121 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6819 (mt0) REVERT: C 185 LYS cc_start: 0.7669 (mmmm) cc_final: 0.7430 (mmmm) REVERT: C 251 PHE cc_start: 0.8050 (t80) cc_final: 0.7805 (t80) REVERT: C 301 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: C 663 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6744 (mp) REVERT: C 743 LYS cc_start: 0.8108 (mttp) cc_final: 0.7803 (ttmm) REVERT: D 30 LEU cc_start: 0.8252 (tt) cc_final: 0.7978 (tt) REVERT: D 33 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: D 234 TYR cc_start: 0.8089 (m-80) cc_final: 0.7836 (m-80) REVERT: D 274 TYR cc_start: 0.7843 (m-80) cc_final: 0.7417 (m-80) REVERT: D 281 SER cc_start: 0.8529 (m) cc_final: 0.7956 (p) REVERT: D 444 LYS cc_start: 0.8127 (mttm) cc_final: 0.7801 (mtpp) REVERT: D 446 LYS cc_start: 0.8170 (mppt) cc_final: 0.7845 (mppt) REVERT: D 518 GLN cc_start: 0.7692 (tp40) cc_final: 0.7217 (tp40) REVERT: D 624 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7598 (p) REVERT: D 690 ILE cc_start: 0.8045 (tp) cc_final: 0.7751 (tt) REVERT: D 737 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6869 (mm-30) REVERT: D 793 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7300 (mtmt) REVERT: D 797 TYR cc_start: 0.6840 (m-80) cc_final: 0.6377 (m-80) REVERT: D 840 LEU cc_start: 0.7788 (mt) cc_final: 0.7474 (mt) REVERT: S 57 LYS cc_start: 0.8015 (mppt) cc_final: 0.7692 (mmtm) REVERT: S 88 TRP cc_start: 0.6222 (t-100) cc_final: 0.5622 (t-100) outliers start: 29 outliers final: 16 residues processed: 322 average time/residue: 0.2795 time to fit residues: 128.0521 Evaluate side-chains 329 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 308 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 663 LEU 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 161 MET 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 185 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14995 Z= 0.201 Angle : 0.531 11.957 20362 Z= 0.273 Chirality : 0.039 0.191 2465 Planarity : 0.004 0.045 2606 Dihedral : 3.609 21.633 2117 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.86 % Allowed : 16.72 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1976 helix: 2.06 (0.15), residues: 1312 sheet: -2.99 (0.76), residues: 40 loop : -1.05 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 33 HIS 0.006 0.001 HIS S 64 PHE 0.029 0.001 PHE C 569 TYR 0.022 0.001 TYR F 128 ARG 0.007 0.000 ARG D 285 *********************** 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 339 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 312 time to evaluate : 1.577 Fit side-chains REVERT: C 95 PHE cc_start: 0.8180 (t80) cc_final: 0.7731 (t80) REVERT: C 97 LYS cc_start: 0.8246 (tppt) cc_final: 0.7824 (tppt) REVERT: C 185 LYS cc_start: 0.7598 (mmmm) cc_final: 0.7388 (mmmm) REVERT: C 251 PHE cc_start: 0.8051 (t80) cc_final: 0.7837 (t80) REVERT: C 301 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: C 663 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6754 (mp) REVERT: C 743 LYS cc_start: 0.8093 (mttp) cc_final: 0.7791 (ttmm) REVERT: D 30 LEU cc_start: 0.8256 (tt) cc_final: 0.7972 (tt) REVERT: D 33 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: D 274 TYR cc_start: 0.7851 (m-80) cc_final: 0.7406 (m-80) REVERT: D 281 SER cc_start: 0.8529 (m) cc_final: 0.7958 (p) REVERT: D 444 LYS cc_start: 0.8126 (mttm) cc_final: 0.7800 (mtpp) REVERT: D 446 LYS cc_start: 0.8181 (mppt) cc_final: 0.7848 (mppt) REVERT: D 518 GLN cc_start: 0.7673 (tp40) cc_final: 0.7205 (tp40) REVERT: D 538 GLU cc_start: 0.7991 (tp30) cc_final: 0.7224 (mm-30) REVERT: D 624 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7585 (p) REVERT: D 690 ILE cc_start: 0.8079 (tp) cc_final: 0.7783 (tt) REVERT: D 729 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7784 (mmmm) REVERT: D 737 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6850 (mm-30) REVERT: D 793 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7286 (mtmt) REVERT: D 797 TYR cc_start: 0.6833 (m-80) cc_final: 0.6380 (m-80) REVERT: D 840 LEU cc_start: 0.7766 (mt) cc_final: 0.7443 (mt) REVERT: S 57 LYS cc_start: 0.8006 (mppt) cc_final: 0.7686 (mmtm) REVERT: S 88 TRP cc_start: 0.6410 (t-100) cc_final: 0.5872 (t-100) outliers start: 27 outliers final: 17 residues processed: 321 average time/residue: 0.2797 time to fit residues: 128.5956 Evaluate side-chains 334 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 313 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 483 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 663 LEU 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 161 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 57 optimal weight: 0.0470 chunk 37 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 174 optimal weight: 50.0000 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14995 Z= 0.171 Angle : 0.523 12.319 20362 Z= 0.270 Chirality : 0.038 0.169 2465 Planarity : 0.004 0.044 2606 Dihedral : 3.511 21.346 2117 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.65 % Allowed : 17.89 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 1976 helix: 2.12 (0.15), residues: 1313 sheet: -2.98 (0.77), residues: 40 loop : -1.03 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 347 HIS 0.005 0.001 HIS S 64 PHE 0.020 0.001 PHE C 402 TYR 0.018 0.001 TYR C 278 ARG 0.007 0.000 ARG D 285 *********************** 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 337 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 313 time to evaluate : 1.524 Fit side-chains REVERT: C 95 PHE cc_start: 0.8154 (t80) cc_final: 0.7700 (t80) REVERT: C 97 LYS cc_start: 0.8262 (tppt) cc_final: 0.7847 (tppt) REVERT: C 185 LYS cc_start: 0.7568 (mmmm) cc_final: 0.7335 (mmmm) REVERT: C 251 PHE cc_start: 0.8024 (t80) cc_final: 0.7769 (t80) REVERT: C 663 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6695 (mp) REVERT: D 30 LEU cc_start: 0.8264 (tt) cc_final: 0.8027 (tt) REVERT: D 31 MET cc_start: 0.7772 (mmm) cc_final: 0.7571 (mmm) REVERT: D 33 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5944 (mp0) REVERT: D 51 LYS cc_start: 0.7406 (tptp) cc_final: 0.6882 (tptp) REVERT: D 234 TYR cc_start: 0.8021 (m-80) cc_final: 0.7753 (m-80) REVERT: D 274 TYR cc_start: 0.7807 (m-80) cc_final: 0.7323 (m-80) REVERT: D 281 SER cc_start: 0.8517 (m) cc_final: 0.7956 (p) REVERT: D 370 GLU cc_start: 0.7097 (tp30) cc_final: 0.6851 (tp30) REVERT: D 444 LYS cc_start: 0.8070 (mttm) cc_final: 0.7751 (mtpp) REVERT: D 446 LYS cc_start: 0.8233 (mppt) cc_final: 0.7883 (mppt) REVERT: D 518 GLN cc_start: 0.7686 (tp40) cc_final: 0.7240 (tp40) REVERT: D 538 GLU cc_start: 0.7973 (tp30) cc_final: 0.7226 (mm-30) REVERT: D 624 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7540 (p) REVERT: D 690 ILE cc_start: 0.8046 (tp) cc_final: 0.7745 (tt) REVERT: D 737 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6838 (mm-30) REVERT: D 793 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7265 (mtmt) REVERT: D 797 TYR cc_start: 0.6831 (m-80) cc_final: 0.6400 (m-80) REVERT: D 840 LEU cc_start: 0.7783 (mt) cc_final: 0.7450 (mt) REVERT: S 57 LYS cc_start: 0.7972 (mppt) cc_final: 0.7643 (mmtm) outliers start: 24 outliers final: 15 residues processed: 324 average time/residue: 0.2840 time to fit residues: 131.2280 Evaluate side-chains 329 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 311 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 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 663 LEU 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 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 183 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 140 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 253 GLN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14995 Z= 0.235 Angle : 0.555 12.686 20362 Z= 0.287 Chirality : 0.040 0.162 2465 Planarity : 0.004 0.044 2606 Dihedral : 3.620 21.562 2117 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.65 % Allowed : 18.24 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1976 helix: 2.04 (0.15), residues: 1310 sheet: -2.53 (0.73), residues: 47 loop : -1.02 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 61 HIS 0.010 0.001 HIS S 64 PHE 0.023 0.001 PHE C 402 TYR 0.020 0.001 TYR C 278 ARG 0.007 0.000 ARG D 285 *********************** 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 335 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 1.735 Fit side-chains REVERT: C 95 PHE cc_start: 0.8189 (t80) cc_final: 0.7727 (t80) REVERT: C 97 LYS cc_start: 0.8237 (tppt) cc_final: 0.7858 (tppt) REVERT: C 177 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7632 (mmmm) REVERT: C 185 LYS cc_start: 0.7623 (mmmm) cc_final: 0.7378 (mmmm) REVERT: C 251 PHE cc_start: 0.8051 (t80) cc_final: 0.7837 (t80) REVERT: C 301 GLU cc_start: 0.7212 (mp0) cc_final: 0.6980 (mp0) REVERT: C 694 GLN cc_start: 0.8007 (tp40) cc_final: 0.7666 (tp40) REVERT: C 712 GLN cc_start: 0.7656 (tt0) cc_final: 0.7436 (tt0) REVERT: C 743 LYS cc_start: 0.8104 (mttp) cc_final: 0.7792 (ttmm) REVERT: D 14 LYS cc_start: 0.8052 (tttp) cc_final: 0.7775 (mtpp) REVERT: D 30 LEU cc_start: 0.8253 (tt) cc_final: 0.7998 (tt) REVERT: D 31 MET cc_start: 0.7773 (mmm) cc_final: 0.7572 (mmm) REVERT: D 33 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: D 274 TYR cc_start: 0.7869 (m-80) cc_final: 0.7359 (m-80) REVERT: D 281 SER cc_start: 0.8542 (m) cc_final: 0.7973 (p) REVERT: D 444 LYS cc_start: 0.8093 (mttm) cc_final: 0.7772 (mtpp) REVERT: D 446 LYS cc_start: 0.8194 (mppt) cc_final: 0.7846 (mppt) REVERT: D 518 GLN cc_start: 0.7712 (tp40) cc_final: 0.7271 (tp40) REVERT: D 538 GLU cc_start: 0.8041 (tp30) cc_final: 0.7213 (mm-30) REVERT: D 624 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7611 (p) REVERT: D 690 ILE cc_start: 0.8038 (tp) cc_final: 0.7763 (tt) REVERT: D 729 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7834 (mmmm) REVERT: D 737 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6855 (mm-30) REVERT: D 793 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7307 (mtmt) REVERT: D 797 TYR cc_start: 0.6872 (m-80) cc_final: 0.6457 (m-80) REVERT: D 840 LEU cc_start: 0.7773 (mt) cc_final: 0.7459 (mt) REVERT: S 57 LYS cc_start: 0.7970 (mppt) cc_final: 0.7628 (mmtm) outliers start: 24 outliers final: 17 residues processed: 322 average time/residue: 0.2877 time to fit residues: 132.0430 Evaluate side-chains 327 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 308 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 LEU 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 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 Chi-restraints excluded: chain S residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 182 optimal weight: 40.0000 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 125 optimal weight: 0.1980 chunk 168 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 121 GLN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14995 Z= 0.184 Angle : 0.548 12.377 20362 Z= 0.281 Chirality : 0.039 0.162 2465 Planarity : 0.004 0.044 2606 Dihedral : 3.550 21.153 2117 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.51 % Allowed : 18.79 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1976 helix: 2.11 (0.15), residues: 1308 sheet: -2.80 (0.76), residues: 42 loop : -1.00 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 61 HIS 0.009 0.001 HIS S 64 PHE 0.020 0.001 PHE C 402 TYR 0.025 0.001 TYR F 128 ARG 0.008 0.000 ARG D 285 ********************** 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 fitting. rotamer outliers: 22 poor density : 312 time to evaluate : 1.652 Fit side-chains REVERT: C 95 PHE cc_start: 0.8163 (t80) cc_final: 0.7692 (t80) REVERT: C 97 LYS cc_start: 0.8241 (tppt) cc_final: 0.7852 (tppt) REVERT: C 177 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7638 (mmmm) REVERT: C 185 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7363 (mmmm) REVERT: C 251 PHE cc_start: 0.8022 (t80) cc_final: 0.7765 (t80) REVERT: C 301 GLU cc_start: 0.7205 (mp0) cc_final: 0.6979 (mp0) REVERT: C 712 GLN cc_start: 0.7696 (tt0) cc_final: 0.7477 (tt0) REVERT: D 14 LYS cc_start: 0.8022 (tttp) cc_final: 0.7742 (mtpp) REVERT: D 30 LEU cc_start: 0.8275 (tt) cc_final: 0.8034 (tt) REVERT: D 31 MET cc_start: 0.7776 (mmm) cc_final: 0.7567 (mmm) REVERT: D 33 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: D 281 SER cc_start: 0.8529 (m) cc_final: 0.7965 (p) REVERT: D 444 LYS cc_start: 0.8065 (mttm) cc_final: 0.7751 (mtpp) REVERT: D 446 LYS cc_start: 0.8189 (mppt) cc_final: 0.7840 (mppt) REVERT: D 518 GLN cc_start: 0.7683 (tp40) cc_final: 0.7252 (tp40) REVERT: D 538 GLU cc_start: 0.7997 (tp30) cc_final: 0.7193 (mm-30) REVERT: D 624 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7531 (p) REVERT: D 690 ILE cc_start: 0.8029 (tp) cc_final: 0.7755 (tt) REVERT: D 729 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7821 (mmmm) REVERT: D 737 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6839 (mm-30) REVERT: D 793 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7292 (mtmt) REVERT: D 797 TYR cc_start: 0.6861 (m-80) cc_final: 0.6444 (m-80) REVERT: D 840 LEU cc_start: 0.7763 (mt) cc_final: 0.7437 (mt) REVERT: S 57 LYS cc_start: 0.7957 (mppt) cc_final: 0.7675 (mmtm) outliers start: 22 outliers final: 16 residues processed: 323 average time/residue: 0.2933 time to fit residues: 133.8908 Evaluate side-chains 332 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 314 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 642 ILE Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain S residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 138 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** 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 = 0.3938 r_free = 0.3938 target = 0.148947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121053 restraints weight = 24315.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124348 restraints weight = 11482.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126518 restraints weight = 6785.673| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14995 Z= 0.195 Angle : 0.549 12.397 20362 Z= 0.282 Chirality : 0.039 0.159 2465 Planarity : 0.004 0.044 2606 Dihedral : 3.539 20.907 2117 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.24 % Allowed : 19.13 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1976 helix: 2.11 (0.15), residues: 1308 sheet: -2.79 (0.75), residues: 42 loop : -1.01 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 61 HIS 0.009 0.001 HIS S 64 PHE 0.021 0.001 PHE C 402 TYR 0.019 0.001 TYR C 278 ARG 0.008 0.000 ARG D 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.85 seconds wall clock time: 62 minutes 29.64 seconds (3749.64 seconds total)