Starting phenix.real_space_refine on Tue Dec 31 11:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gu6_34270/12_2024/8gu6_34270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gu6_34270/12_2024/8gu6_34270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gu6_34270/12_2024/8gu6_34270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gu6_34270/12_2024/8gu6_34270.map" model { file = "/net/cci-nas-00/data/ceres_data/8gu6_34270/12_2024/8gu6_34270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gu6_34270/12_2024/8gu6_34270.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 50 5.49 5 S 51 5.16 5 C 9590 2.51 5 N 2670 2.21 5 O 2896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15261 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 4880 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 19, 'TRANS': 639} Chain breaks: 4 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 15, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 316 Chain: "A" Number of atoms: 9314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 9314 Classifications: {'peptide': 1211} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 59, 'TRANS': 1151} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 385 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 14, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 34, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 14} Chain: "J" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8188 SG CYS A 491 42.410 50.382 109.592 1.00 56.88 S ATOM 8256 SG CYS A 501 42.340 50.002 113.239 1.00 43.26 S ATOM 8270 SG CYS A 503 39.054 50.135 111.347 1.00 51.40 S ATOM 8292 SG CYS A 506 41.174 47.041 110.957 1.00 42.41 S ATOM 5526 SG CYS A 88 41.869 29.986 135.607 1.00 52.94 S ATOM 5769 SG CYS A 121 42.592 27.562 138.440 1.00 80.14 S ATOM 5800 SG CYS A 127 41.344 26.344 135.032 1.00 50.36 S ATOM 5824 SG CYS A 130 44.895 27.615 135.412 1.00 49.35 S ATOM 10157 SG CYS A 750 48.196 66.675 85.818 1.00 94.35 S ATOM 10170 SG CYS A 752 45.399 65.843 83.413 1.00 72.34 S ATOM 10192 SG CYS A 755 47.298 62.993 84.983 1.00 66.08 S ATOM 12065 SG CYS A1018 57.375 61.363 49.287 1.00 82.93 S ATOM 12218 SG CYS A1406 57.984 62.296 52.978 1.00 87.64 S ATOM 12269 SG CYS A1414 57.266 64.947 50.377 1.00 79.23 S ATOM 12286 SG CYS A1417 54.544 62.425 51.493 1.00 64.66 S Time building chain proxies: 8.97, per 1000 atoms: 0.59 Number of scatterers: 15261 At special positions: 0 Unit cell: (101.65, 95, 158.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 51 16.00 P 50 15.00 O 2896 8.00 N 2670 7.00 C 9590 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: 4.13 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " Number of angles added : 21 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 41.7% alpha, 11.9% beta 11 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'D' and resid 15 through 33 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.938A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 82 removed outlier: 3.643A pdb=" N ILE D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 110 removed outlier: 3.550A pdb=" N LYS D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.611A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.942A pdb=" N LYS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.703A pdb=" N LYS D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 246 removed outlier: 4.095A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 3.602A pdb=" N PHE D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 297 Processing helix chain 'D' and resid 302 through 322 removed outlier: 3.559A pdb=" N LYS D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 339 through 359 removed outlier: 3.601A pdb=" N GLU D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 473 removed outlier: 3.501A pdb=" N PHE D 473 " --> pdb=" O PRO D 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 470 through 473' Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 509 through 514 removed outlier: 4.261A pdb=" N ASN D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS D 514 " --> pdb=" O PHE D 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 509 through 514' Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 566 through 572 Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 628 through 632 removed outlier: 3.550A pdb=" N VAL D 632 " --> pdb=" O THR D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 653 removed outlier: 3.684A pdb=" N ALA D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.851A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 691 removed outlier: 4.165A pdb=" N LYS D 689 " --> pdb=" O ASN D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 removed outlier: 3.999A pdb=" N ALA D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.404A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.563A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.548A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Processing helix chain 'A' and resid 292 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.582A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 624 removed outlier: 3.631A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.579A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 687 through 693 removed outlier: 3.546A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 873 through 881 removed outlier: 3.670A pdb=" N MET A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.889A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.745A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1399 removed outlier: 3.574A pdb=" N LYS A1398 " --> pdb=" O LEU A1395 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A1399 " --> pdb=" O GLY A1396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1395 through 1399' Processing helix chain 'A' and resid 1408 through 1412 removed outlier: 3.625A pdb=" N ASP A1411 " --> pdb=" O GLY A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.064A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.791A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.779A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1588 Processing helix chain 'A' and resid 1590 through 1601 removed outlier: 3.541A pdb=" N GLU A1600 " --> pdb=" O GLN A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1675 through 1681 Processing sheet with id=AA1, first strand: chain 'D' and resid 425 through 431 removed outlier: 3.765A pdb=" N ASP D 420 " --> pdb=" O SER D 425 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS D 516 " --> pdb=" O PHE D 709 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER D 711 " --> pdb=" O CYS D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 562 through 563 removed outlier: 6.583A pdb=" N VAL D 537 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU D 583 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 539 " --> pdb=" O LEU D 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 597 through 598 Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.507A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.507A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.008A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.701A pdb=" N PHE A 192 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 514 removed outlier: 3.515A pdb=" N PHE A 557 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.258A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.587A pdb=" N SER A 517 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB5, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.872A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.872A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.161A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 920 through 921 removed outlier: 3.672A pdb=" N TYR A 921 " --> pdb=" O ASP A1642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC1, first strand: chain 'A' and resid 1519 through 1522 removed outlier: 6.819A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.917A pdb=" N GLU A1510 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A1509 " --> pdb=" O LEU A1454 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 991 through 992 Processing sheet with id=AC4, first strand: chain 'A' and resid 1647 through 1648 removed outlier: 6.753A pdb=" N VAL A1647 " --> pdb=" O TYR A1663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 589 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 7.17 Time building geometry restraints manager: 4.76 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: 4328 1.33 - 1.45: 2854 1.45 - 1.57: 8353 1.57 - 1.69: 98 1.69 - 1.81: 69 Bond restraints: 15702 Sorted by residual: bond pdb=" C SER A 910 " pdb=" N PRO A 911 " ideal model delta sigma weight residual 1.336 1.350 -0.014 9.80e-03 1.04e+04 1.96e+00 bond pdb=" CB GLU D 398 " pdb=" CG GLU D 398 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.16e-01 bond pdb=" C PRO D 700 " pdb=" N PRO D 701 " ideal model delta sigma weight residual 1.336 1.345 -0.010 1.23e-02 6.61e+03 6.44e-01 bond pdb=" CG1 ILE D 45 " pdb=" CD1 ILE D 45 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.92e-01 bond pdb=" CB GLU D 23 " pdb=" CG GLU D 23 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.85e-01 ... (remaining 15697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 21432 3.02 - 6.04: 69 6.04 - 9.06: 4 9.06 - 12.08: 0 12.08 - 15.10: 1 Bond angle restraints: 21506 Sorted by residual: angle pdb=" O4' G C 11 " pdb=" C1' G C 11 " pdb=" N9 G C 11 " ideal model delta sigma weight residual 108.20 115.61 -7.41 1.50e+00 4.44e-01 2.44e+01 angle pdb=" CA LEU A 366 " pdb=" CB LEU A 366 " pdb=" CG LEU A 366 " ideal model delta sigma weight residual 116.30 131.40 -15.10 3.50e+00 8.16e-02 1.86e+01 angle pdb=" O4' A C -2 " pdb=" C1' A C -2 " pdb=" N9 A C -2 " ideal model delta sigma weight residual 108.20 112.52 -4.32 1.50e+00 4.44e-01 8.29e+00 angle pdb=" N GLU A1441 " pdb=" CA GLU A1441 " pdb=" C GLU A1441 " ideal model delta sigma weight residual 110.97 114.10 -3.13 1.09e+00 8.42e-01 8.23e+00 angle pdb=" N LEU A 366 " pdb=" CA LEU A 366 " pdb=" CB LEU A 366 " ideal model delta sigma weight residual 110.28 114.68 -4.40 1.55e+00 4.16e-01 8.07e+00 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 8925 35.68 - 71.36: 417 71.36 - 107.04: 21 107.04 - 142.72: 2 142.72 - 178.40: 2 Dihedral angle restraints: 9367 sinusoidal: 3991 harmonic: 5376 Sorted by residual: dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual 232.00 53.60 178.40 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 10 " pdb=" C1' U C 10 " pdb=" N1 U C 10 " pdb=" C2 U C 10 " ideal model delta sinusoidal sigma weight residual -128.00 44.11 -172.11 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U C -15 " pdb=" C1' U C -15 " pdb=" N1 U C -15 " pdb=" C2 U C -15 " ideal model delta sinusoidal sigma weight residual -160.00 -91.17 -68.83 1 1.50e+01 4.44e-03 2.73e+01 ... (remaining 9364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2239 0.073 - 0.146: 186 0.146 - 0.218: 6 0.218 - 0.291: 0 0.291 - 0.364: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" C1' G C 11 " pdb=" O4' G C 11 " pdb=" C2' G C 11 " pdb=" N9 G C 11 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1' A C -2 " pdb=" O4' A C -2 " pdb=" C2' A C -2 " pdb=" N9 A C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB ILE D 80 " pdb=" CA ILE D 80 " pdb=" CG1 ILE D 80 " pdb=" CG2 ILE D 80 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2429 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 11 " -0.047 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G C 11 " 0.056 2.00e-02 2.50e+03 pdb=" C8 G C 11 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C 11 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 11 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G C 11 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G C 11 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G C 11 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 11 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G C 11 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1475 " -0.051 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO A1476 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A1476 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1476 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A C 3 " -0.031 2.00e-02 2.50e+03 1.45e-02 5.78e+00 pdb=" N9 A C 3 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A C 3 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A C 3 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A C 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 3 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 3 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A C 3 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A C 3 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A C 3 " 0.006 2.00e-02 2.50e+03 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 295 2.65 - 3.21: 14000 3.21 - 3.78: 25283 3.78 - 4.34: 34607 4.34 - 4.90: 56189 Nonbonded interactions: 130374 Sorted by model distance: nonbonded pdb=" O GLY A 186 " pdb=" O2' C C -1 " model vdw 2.091 3.040 nonbonded pdb=" O LYS D 321 " pdb=" OH TYR D 643 " model vdw 2.136 3.040 nonbonded pdb=" O ALA A 685 " pdb=" O2' U C 5 " model vdw 2.163 3.040 nonbonded pdb=" O ASN A 179 " pdb=" O2' G C -4 " model vdw 2.189 3.040 nonbonded pdb=" N THR D 629 " pdb=" O THR D 660 " model vdw 2.194 3.120 ... (remaining 130369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 45.030 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.002 0.033 15702 Z= 0.157 Angle : 0.534 15.101 21506 Z= 0.283 Chirality : 0.040 0.364 2432 Planarity : 0.004 0.078 2558 Dihedral : 18.657 178.395 5903 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.14 % Allowed : 28.99 % Favored : 70.86 % 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: -0.34 (0.19), residues: 1832 helix: 1.28 (0.21), residues: 647 sheet: -0.79 (0.35), residues: 221 loop : -1.15 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 165 HIS 0.012 0.001 HIS A1621 PHE 0.019 0.001 PHE A1011 TYR 0.022 0.001 TYR D 259 ARG 0.007 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 1.660 Fit side-chains REVERT: D 420 ASP cc_start: 0.7551 (p0) cc_final: 0.7033 (p0) REVERT: D 630 ASP cc_start: 0.7911 (p0) cc_final: 0.7527 (p0) REVERT: D 666 SER cc_start: 0.7254 (m) cc_final: 0.6776 (p) REVERT: A 308 GLU cc_start: 0.6421 (pm20) cc_final: 0.5741 (pt0) REVERT: A 762 HIS cc_start: 0.7015 (m170) cc_final: 0.6804 (m-70) REVERT: A 771 ASP cc_start: 0.8249 (m-30) cc_final: 0.7603 (m-30) REVERT: A 995 GLU cc_start: 0.7704 (pt0) cc_final: 0.7268 (pt0) outliers start: 2 outliers final: 2 residues processed: 169 average time/residue: 0.3303 time to fit residues: 80.2878 Evaluate side-chains 155 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 195 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN A 306 HIS ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS A1494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15702 Z= 0.242 Angle : 0.555 8.515 21506 Z= 0.292 Chirality : 0.042 0.421 2432 Planarity : 0.004 0.060 2558 Dihedral : 15.049 174.967 2777 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.76 % Allowed : 26.46 % Favored : 69.78 % 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: -0.36 (0.19), residues: 1832 helix: 1.25 (0.20), residues: 662 sheet: -0.92 (0.35), residues: 215 loop : -1.16 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 330 HIS 0.010 0.001 HIS A1621 PHE 0.015 0.001 PHE D 547 TYR 0.016 0.001 TYR A1595 ARG 0.005 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 1.689 Fit side-chains REVERT: D 231 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6617 (ttp-110) REVERT: D 542 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: A 308 GLU cc_start: 0.6533 (pm20) cc_final: 0.5918 (pt0) REVERT: A 389 TYR cc_start: 0.8046 (t80) cc_final: 0.7802 (t80) REVERT: A 877 LYS cc_start: 0.7161 (tptm) cc_final: 0.6843 (mtpp) REVERT: A 927 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7119 (tt) REVERT: A 1487 TRP cc_start: 0.7772 (p-90) cc_final: 0.7491 (p-90) outliers start: 52 outliers final: 24 residues processed: 200 average time/residue: 0.3171 time to fit residues: 91.5933 Evaluate side-chains 169 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 153 optimal weight: 0.0980 chunk 171 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15702 Z= 0.238 Angle : 0.541 9.219 21506 Z= 0.283 Chirality : 0.042 0.428 2432 Planarity : 0.004 0.051 2558 Dihedral : 14.958 175.441 2772 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.70 % Allowed : 25.31 % Favored : 69.99 % 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: -0.39 (0.19), residues: 1832 helix: 1.25 (0.20), residues: 665 sheet: -1.02 (0.35), residues: 215 loop : -1.18 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 330 HIS 0.007 0.001 HIS A1621 PHE 0.014 0.001 PHE D 289 TYR 0.015 0.001 TYR D 607 ARG 0.006 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: D 260 ARG cc_start: 0.6808 (mtt90) cc_final: 0.6603 (mtt90) REVERT: D 542 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: D 585 HIS cc_start: 0.6194 (OUTLIER) cc_final: 0.5803 (p-80) REVERT: A 107 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8099 (pttt) REVERT: A 389 TYR cc_start: 0.8073 (t80) cc_final: 0.7807 (t80) REVERT: A 605 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7926 (ptpt) REVERT: A 877 LYS cc_start: 0.7231 (tptm) cc_final: 0.6836 (mtpp) REVERT: A 927 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7202 (tt) REVERT: A 1487 TRP cc_start: 0.7939 (p-90) cc_final: 0.7696 (p-90) outliers start: 65 outliers final: 38 residues processed: 202 average time/residue: 0.2976 time to fit residues: 88.4913 Evaluate side-chains 189 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN A1494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15702 Z= 0.400 Angle : 0.626 8.699 21506 Z= 0.324 Chirality : 0.045 0.428 2432 Planarity : 0.004 0.046 2558 Dihedral : 15.073 173.115 2772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 6.44 % Allowed : 24.01 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1832 helix: 1.02 (0.20), residues: 666 sheet: -1.45 (0.32), residues: 227 loop : -1.27 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 330 HIS 0.006 0.001 HIS A1621 PHE 0.019 0.002 PHE A 358 TYR 0.017 0.002 TYR D 607 ARG 0.005 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 152 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: D 260 ARG cc_start: 0.6867 (mtt90) cc_final: 0.6653 (mtt90) REVERT: D 542 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: D 585 HIS cc_start: 0.6427 (OUTLIER) cc_final: 0.6036 (p-80) REVERT: A 107 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8250 (pttt) REVERT: A 141 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7922 (mttp) REVERT: A 308 GLU cc_start: 0.6334 (pm20) cc_final: 0.5822 (pt0) REVERT: A 605 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7879 (ptpt) REVERT: A 927 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7287 (tt) REVERT: A 972 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6867 (mm-30) outliers start: 89 outliers final: 43 residues processed: 219 average time/residue: 0.3151 time to fit residues: 100.9485 Evaluate side-chains 190 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 675 TRP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1582 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 133 ASN ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15702 Z= 0.182 Angle : 0.527 11.292 21506 Z= 0.275 Chirality : 0.041 0.421 2432 Planarity : 0.004 0.048 2558 Dihedral : 14.936 177.739 2772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.56 % Allowed : 25.96 % Favored : 69.49 % 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: -0.45 (0.19), residues: 1832 helix: 1.26 (0.20), residues: 667 sheet: -1.26 (0.33), residues: 217 loop : -1.22 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1487 HIS 0.006 0.001 HIS A1621 PHE 0.016 0.001 PHE D 491 TYR 0.014 0.001 TYR D 607 ARG 0.006 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 1.769 Fit side-chains REVERT: D 260 ARG cc_start: 0.6771 (mtt90) cc_final: 0.6540 (mtt90) REVERT: D 398 GLU cc_start: 0.8439 (tp30) cc_final: 0.7999 (tt0) REVERT: D 542 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: D 585 HIS cc_start: 0.6168 (OUTLIER) cc_final: 0.5865 (p-80) REVERT: A 308 GLU cc_start: 0.6453 (pm20) cc_final: 0.5844 (pt0) REVERT: A 765 SER cc_start: 0.8439 (t) cc_final: 0.7894 (p) REVERT: A 877 LYS cc_start: 0.7163 (tptm) cc_final: 0.6751 (mtpp) REVERT: A 927 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7358 (tt) REVERT: A 1487 TRP cc_start: 0.8093 (p-90) cc_final: 0.7851 (p-90) outliers start: 63 outliers final: 36 residues processed: 201 average time/residue: 0.3007 time to fit residues: 89.5687 Evaluate side-chains 183 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1517 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15702 Z= 0.247 Angle : 0.551 11.408 21506 Z= 0.286 Chirality : 0.042 0.420 2432 Planarity : 0.004 0.045 2558 Dihedral : 14.894 174.838 2772 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.06 % Allowed : 25.96 % Favored : 68.98 % 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: -0.46 (0.19), residues: 1832 helix: 1.27 (0.20), residues: 669 sheet: -1.31 (0.33), residues: 217 loop : -1.24 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 330 HIS 0.009 0.001 HIS A1484 PHE 0.014 0.001 PHE D 491 TYR 0.015 0.001 TYR D 607 ARG 0.006 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 151 time to evaluate : 1.786 Fit side-chains REVERT: D 260 ARG cc_start: 0.6739 (mtt90) cc_final: 0.6521 (mtt90) REVERT: D 542 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: D 585 HIS cc_start: 0.6222 (OUTLIER) cc_final: 0.5805 (p-80) REVERT: A 141 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7864 (mttp) REVERT: A 214 GLU cc_start: 0.7239 (pm20) cc_final: 0.7022 (mm-30) REVERT: A 308 GLU cc_start: 0.6407 (pm20) cc_final: 0.5864 (pt0) REVERT: A 605 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8036 (ptpt) REVERT: A 765 SER cc_start: 0.8555 (t) cc_final: 0.8015 (p) REVERT: A 877 LYS cc_start: 0.7190 (tptm) cc_final: 0.6669 (mtpp) REVERT: A 927 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7357 (tt) REVERT: A 972 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6444 (mm-30) REVERT: A 1441 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6451 (mm-30) REVERT: A 1487 TRP cc_start: 0.8126 (p-90) cc_final: 0.7872 (p-90) outliers start: 70 outliers final: 48 residues processed: 207 average time/residue: 0.2992 time to fit residues: 91.1794 Evaluate side-chains 201 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 104 optimal weight: 0.0470 chunk 134 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15702 Z= 0.178 Angle : 0.519 12.063 21506 Z= 0.269 Chirality : 0.041 0.418 2432 Planarity : 0.004 0.044 2558 Dihedral : 14.840 177.649 2772 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.27 % Allowed : 26.68 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1832 helix: 1.41 (0.20), residues: 667 sheet: -1.19 (0.34), residues: 209 loop : -1.23 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 330 HIS 0.007 0.001 HIS A1484 PHE 0.015 0.001 PHE D 491 TYR 0.014 0.001 TYR D 607 ARG 0.006 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 153 time to evaluate : 1.714 Fit side-chains REVERT: D 260 ARG cc_start: 0.6726 (mtt90) cc_final: 0.6500 (mtt90) REVERT: D 398 GLU cc_start: 0.8410 (tp30) cc_final: 0.7994 (tt0) REVERT: D 542 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: D 585 HIS cc_start: 0.6119 (OUTLIER) cc_final: 0.5762 (p-80) REVERT: D 630 ASP cc_start: 0.7749 (p0) cc_final: 0.7340 (p0) REVERT: A 308 GLU cc_start: 0.6308 (pm20) cc_final: 0.5789 (pt0) REVERT: A 361 MET cc_start: 0.6463 (tpp) cc_final: 0.6194 (mmp) REVERT: A 389 TYR cc_start: 0.7998 (t80) cc_final: 0.7727 (t80) REVERT: A 765 SER cc_start: 0.8495 (t) cc_final: 0.8001 (p) REVERT: A 877 LYS cc_start: 0.7109 (tptm) cc_final: 0.6682 (mtpp) REVERT: A 927 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7339 (tt) REVERT: A 972 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6343 (mm-30) REVERT: A 1441 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6303 (mm-30) REVERT: A 1529 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7281 (tp30) outliers start: 59 outliers final: 42 residues processed: 198 average time/residue: 0.2899 time to fit residues: 87.0867 Evaluate side-chains 193 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15702 Z= 0.240 Angle : 0.548 12.086 21506 Z= 0.283 Chirality : 0.042 0.410 2432 Planarity : 0.004 0.044 2558 Dihedral : 14.807 174.676 2772 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.99 % Allowed : 26.10 % Favored : 68.91 % 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: -0.43 (0.19), residues: 1832 helix: 1.34 (0.20), residues: 672 sheet: -1.32 (0.33), residues: 225 loop : -1.25 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 330 HIS 0.007 0.001 HIS A1484 PHE 0.018 0.001 PHE D 289 TYR 0.015 0.001 TYR D 607 ARG 0.008 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 1.684 Fit side-chains REVERT: D 260 ARG cc_start: 0.6734 (mtt90) cc_final: 0.6499 (mtt90) REVERT: D 398 GLU cc_start: 0.8404 (tp30) cc_final: 0.8027 (tt0) REVERT: D 542 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: D 585 HIS cc_start: 0.6204 (OUTLIER) cc_final: 0.5757 (p-80) REVERT: D 630 ASP cc_start: 0.7757 (p0) cc_final: 0.7349 (p0) REVERT: A 308 GLU cc_start: 0.6375 (pm20) cc_final: 0.5887 (pt0) REVERT: A 389 TYR cc_start: 0.8055 (t80) cc_final: 0.7783 (t80) REVERT: A 605 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8100 (ptpt) REVERT: A 719 ARG cc_start: 0.8368 (mmt-90) cc_final: 0.8076 (mmt-90) REVERT: A 765 SER cc_start: 0.8572 (t) cc_final: 0.8045 (p) REVERT: A 815 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8158 (mmtp) REVERT: A 877 LYS cc_start: 0.7197 (tptm) cc_final: 0.6751 (mtpp) REVERT: A 927 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7382 (tt) REVERT: A 972 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6433 (mm-30) REVERT: A 1441 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6388 (mm-30) REVERT: A 1487 TRP cc_start: 0.7947 (p-90) cc_final: 0.7661 (p-90) outliers start: 69 outliers final: 52 residues processed: 209 average time/residue: 0.3076 time to fit residues: 94.3970 Evaluate side-chains 207 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 154 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS A1494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15702 Z= 0.174 Angle : 0.519 12.919 21506 Z= 0.268 Chirality : 0.041 0.408 2432 Planarity : 0.004 0.043 2558 Dihedral : 14.748 177.432 2772 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.56 % Allowed : 26.61 % Favored : 68.84 % 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: -0.30 (0.19), residues: 1832 helix: 1.48 (0.20), residues: 670 sheet: -1.19 (0.35), residues: 211 loop : -1.21 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 330 HIS 0.006 0.001 HIS A1484 PHE 0.017 0.001 PHE D 289 TYR 0.013 0.001 TYR D 607 ARG 0.007 0.000 ARG A1581 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.684 Fit side-chains REVERT: D 260 ARG cc_start: 0.6714 (mtt90) cc_final: 0.6476 (mtt90) REVERT: D 542 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: D 585 HIS cc_start: 0.6053 (OUTLIER) cc_final: 0.5704 (p-80) REVERT: A 141 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7862 (mttp) REVERT: A 308 GLU cc_start: 0.6290 (pm20) cc_final: 0.5784 (pt0) REVERT: A 389 TYR cc_start: 0.7994 (t80) cc_final: 0.7727 (t80) REVERT: A 765 SER cc_start: 0.8514 (t) cc_final: 0.8042 (p) REVERT: A 815 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8273 (mmtp) REVERT: A 877 LYS cc_start: 0.7081 (tptm) cc_final: 0.6534 (mtpp) REVERT: A 927 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7387 (tt) REVERT: A 972 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6340 (mm-30) REVERT: A 1441 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6363 (mm-30) REVERT: A 1487 TRP cc_start: 0.7851 (p-90) cc_final: 0.7479 (p-90) outliers start: 63 outliers final: 44 residues processed: 206 average time/residue: 0.3193 time to fit residues: 96.7328 Evaluate side-chains 198 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15702 Z= 0.210 Angle : 0.538 12.770 21506 Z= 0.277 Chirality : 0.041 0.404 2432 Planarity : 0.004 0.044 2558 Dihedral : 14.724 175.413 2772 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.19 % Allowed : 27.04 % Favored : 68.76 % 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: -0.34 (0.19), residues: 1832 helix: 1.42 (0.20), residues: 672 sheet: -1.29 (0.33), residues: 228 loop : -1.19 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1530 HIS 0.006 0.001 HIS A1484 PHE 0.018 0.001 PHE D 289 TYR 0.015 0.001 TYR A 702 ARG 0.007 0.000 ARG A1581 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 1.761 Fit side-chains REVERT: D 260 ARG cc_start: 0.6709 (mtt90) cc_final: 0.6477 (mtt90) REVERT: D 358 ASP cc_start: 0.7518 (m-30) cc_final: 0.6982 (m-30) REVERT: D 398 GLU cc_start: 0.8382 (tp30) cc_final: 0.7937 (tt0) REVERT: D 542 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: D 585 HIS cc_start: 0.6111 (OUTLIER) cc_final: 0.5676 (p-80) REVERT: A 141 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7880 (mttp) REVERT: A 308 GLU cc_start: 0.6303 (pm20) cc_final: 0.5799 (pt0) REVERT: A 389 TYR cc_start: 0.8040 (t80) cc_final: 0.7768 (t80) REVERT: A 765 SER cc_start: 0.8560 (t) cc_final: 0.8056 (p) REVERT: A 815 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8149 (mmtp) REVERT: A 877 LYS cc_start: 0.7119 (tptm) cc_final: 0.6557 (mtpp) REVERT: A 927 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7399 (tt) REVERT: A 972 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6493 (mm-30) REVERT: A 1441 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6394 (mm-30) REVERT: A 1487 TRP cc_start: 0.7954 (p-90) cc_final: 0.7545 (p-90) outliers start: 58 outliers final: 48 residues processed: 193 average time/residue: 0.2988 time to fit residues: 85.8678 Evaluate side-chains 199 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 671 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.176822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131710 restraints weight = 16883.195| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.09 r_work: 0.3372 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15702 Z= 0.197 Angle : 0.531 13.334 21506 Z= 0.273 Chirality : 0.041 0.395 2432 Planarity : 0.004 0.044 2558 Dihedral : 14.693 176.104 2772 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.41 % Allowed : 27.04 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1832 helix: 1.45 (0.20), residues: 673 sheet: -1.24 (0.34), residues: 218 loop : -1.19 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1530 HIS 0.006 0.001 HIS A1484 PHE 0.017 0.001 PHE D 289 TYR 0.014 0.001 TYR D 607 ARG 0.007 0.000 ARG A1581 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.83 seconds wall clock time: 62 minutes 21.84 seconds (3741.84 seconds total)