Starting phenix.real_space_refine on Thu Aug 6 13:57:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_34270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_34270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_34270.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_34270.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_34270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_34270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gu6_34270/08_2026/8gu6_34270.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'ARG:plan': 8, 'GLU:plan': 19, 'ASP:plan': 22, 'ASN:plan1': 15, 'PHE:plan': 5, 'GLN:plan1': 4, 'TYR:plan': 2, 'HIS:plan': 4, 'TRP:plan': 1} 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: {'GLU:plan': 34, 'ASP:plan': 26, 'GLN:plan1': 5, 'ASN:plan1': 14, 'ARG:plan': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNAv2': 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: {'RNAv2': 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: 2.66, per 1000 atoms: 0.17 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: 1.32 Conformation dependent library (CDL) restraints added in 617.2 milliseconds 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: 1.77 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: 3.20 Time building geometry restraints manager: 1.77 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=" C4' G C 11 " pdb=" C3' G C 11 " ideal model delta sigma weight residual 1.520 1.538 -0.018 2.00e-02 2.50e+03 8.47e-01 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=" C1' A C 3 " pdb=" N9 A C 3 " ideal model delta sigma weight residual 1.478 1.462 0.016 2.00e-02 2.50e+03 6.01e-01 ... (remaining 15697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 21338 3.02 - 6.04: 163 6.04 - 9.06: 4 9.06 - 12.08: 0 12.08 - 15.10: 1 Bond angle restraints: 21506 Sorted by residual: 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' G C 11 " pdb=" C1' G C 11 " pdb=" N9 G C 11 " ideal model delta sigma weight residual 108.50 115.61 -7.11 2.00e+00 2.50e-01 1.26e+01 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 angle pdb=" C3' G C 11 " pdb=" C2' G C 11 " pdb=" O2' G C 11 " ideal model delta sigma weight residual 109.80 115.37 -5.57 2.00e+00 2.50e-01 7.75e+00 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 7664 17.42 - 34.85: 1052 34.85 - 52.27: 322 52.27 - 69.70: 127 69.70 - 87.12: 24 Dihedral angle restraints: 9189 sinusoidal: 3813 harmonic: 5376 Sorted by residual: dihedral pdb=" C4' G C 11 " pdb=" C3' G C 11 " pdb=" C2' G C 11 " pdb=" C1' G C 11 " ideal model delta sinusoidal sigma weight residual 36.34 -38.17 74.51 1 3.10e+00 1.04e-01 7.32e+02 dihedral pdb=" C4' G C -4 " pdb=" C3' G C -4 " pdb=" C2' G C -4 " pdb=" C1' G C -4 " ideal model delta sinusoidal sigma weight residual 36.34 -36.18 72.52 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" C4' A C -13 " pdb=" C3' A C -13 " pdb=" C2' A C -13 " pdb=" C1' A C -13 " ideal model delta sinusoidal sigma weight residual 36.34 -35.98 72.33 1 3.10e+00 1.04e-01 6.96e+02 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2171 0.076 - 0.153: 164 0.153 - 0.229: 35 0.229 - 0.306: 59 0.306 - 0.382: 3 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 2.46 2.07 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C3' G C 11 " pdb=" C4' G C 11 " pdb=" O3' G C 11 " pdb=" C2' G C 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2' A C 3 " pdb=" C3' A C 3 " pdb=" O2' A C 3 " pdb=" C1' A C 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.640 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15718 Z= 0.117 Angle : 0.634 15.101 21527 Z= 0.306 Chirality : 0.062 0.382 2432 Planarity : 0.004 0.078 2558 Dihedral : 18.675 87.122 5725 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (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 ARG 0.007 0.000 ARG A1581 TYR 0.022 0.001 TYR D 259 PHE 0.019 0.001 PHE A1011 TRP 0.022 0.001 TRP D 165 HIS 0.012 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15702) covalent geometry : angle 0.62960 / 0.31 (21506) hydrogen bonds : bond 0.18317 / 12.96 ( 606) hydrogen bonds : angle 6.53707 / 4.78 ( 1705) metal coordination : bond 0.01080 / 0.89 ( 16) metal coordination : angle 2.43043 / 1.72 ( 21) *********************** 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 : 0.511 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: 0.1300 time to fit residues: 31.9610 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 : 0.365 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138486 restraints weight = 17037.795| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.01 r_work: 0.3427 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15718 Z= 0.171 Angle : 0.841 14.616 21527 Z= 0.374 Chirality : 0.080 1.059 2432 Planarity : 0.004 0.060 2558 Dihedral : 11.707 170.671 2599 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.90 % Allowed : 26.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1832 helix: 1.27 (0.20), residues: 662 sheet: -0.88 (0.35), residues: 215 loop : -1.17 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 476 TYR 0.016 0.001 TYR D 607 PHE 0.014 0.001 PHE D 547 TRP 0.026 0.001 TRP A 330 HIS 0.010 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (15702) covalent geometry : angle 0.83703 / 0.37 (21506) hydrogen bonds : bond 0.04185 / 2.81 ( 606) hydrogen bonds : angle 4.95711 / 3.65 ( 1705) metal coordination : bond 0.00950 / 0.75 ( 16) metal coordination : angle 2.89131 / 2.16 ( 21) *********************** 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 216 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.375 Fit side-chains REVERT: D 231 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.6647 (ttp-110) REVERT: D 542 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6295 (m-80) REVERT: A 107 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8289 (pttt) REVERT: A 141 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7313 (mttp) REVERT: A 308 GLU cc_start: 0.6722 (pm20) cc_final: 0.5904 (pt0) REVERT: A 389 TYR cc_start: 0.8377 (t80) cc_final: 0.8098 (t80) REVERT: A 877 LYS cc_start: 0.7073 (tptm) cc_final: 0.6664 (mtpp) REVERT: A 927 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7075 (tt) outliers start: 54 outliers final: 25 residues processed: 200 average time/residue: 0.1212 time to fit residues: 35.0413 Evaluate side-chains 175 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 D residue 594 PHE Chi-restraints excluded: chain A residue 45 THR 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 150 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 684 THR 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 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 1507 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 130 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138277 restraints weight = 17143.964| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.06 r_work: 0.3437 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15718 Z= 0.153 Angle : 0.734 11.971 21527 Z= 0.334 Chirality : 0.065 0.783 2432 Planarity : 0.004 0.051 2558 Dihedral : 11.972 179.380 2594 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.70 % Allowed : 25.16 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1832 helix: 1.28 (0.20), residues: 666 sheet: -0.94 (0.35), residues: 215 loop : -1.19 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 476 TYR 0.015 0.001 TYR D 607 PHE 0.014 0.001 PHE D 289 TRP 0.032 0.001 TRP A 330 HIS 0.007 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15702) covalent geometry : angle 0.72927 / 0.33 (21506) hydrogen bonds : bond 0.03757 / 2.51 ( 606) hydrogen bonds : angle 4.58034 / 3.36 ( 1705) metal coordination : bond 0.01215 / 0.97 ( 16) metal coordination : angle 2.87561 / 2.13 ( 21) *********************** 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 225 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: D 260 ARG cc_start: 0.6914 (mtt90) cc_final: 0.6700 (mtt90) REVERT: D 278 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.8015 (p-90) REVERT: D 542 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: D 585 HIS cc_start: 0.6213 (OUTLIER) cc_final: 0.5880 (p-80) REVERT: A 141 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7182 (mttp) REVERT: A 389 TYR cc_start: 0.8332 (t80) cc_final: 0.8084 (t80) REVERT: A 877 LYS cc_start: 0.7072 (tptm) cc_final: 0.6614 (mtpp) REVERT: A 927 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7152 (tt) REVERT: A 1463 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.6988 (ttp-170) REVERT: A 1487 TRP cc_start: 0.8080 (p-90) cc_final: 0.7589 (p-90) outliers start: 65 outliers final: 35 residues processed: 207 average time/residue: 0.1081 time to fit residues: 33.2325 Evaluate side-chains 194 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 278 TRP 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 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 131 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 150 ASP 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 540 VAL Chi-restraints excluded: chain A residue 542 ASP 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 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 176 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 162 optimal weight: 0.0050 chunk 110 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.180314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140633 restraints weight = 17021.559| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.98 r_work: 0.3464 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15718 Z= 0.132 Angle : 0.687 10.239 21527 Z= 0.314 Chirality : 0.059 0.604 2432 Planarity : 0.004 0.046 2558 Dihedral : 11.945 177.670 2594 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.71 % Allowed : 23.72 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1832 helix: 1.38 (0.20), residues: 667 sheet: -0.91 (0.35), residues: 209 loop : -1.17 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.013 0.001 PHE D 289 TRP 0.024 0.001 TRP A 330 HIS 0.007 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15702) covalent geometry : angle 0.68148 / 0.31 (21506) hydrogen bonds : bond 0.03418 / 2.27 ( 606) hydrogen bonds : angle 4.35830 / 3.20 ( 1705) metal coordination : bond 0.01065 / 0.86 ( 16) metal coordination : angle 2.92656 / 2.12 ( 21) *********************** 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 236 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 157 time to evaluate : 0.355 Fit side-chains REVERT: D 260 ARG cc_start: 0.6913 (mtt90) cc_final: 0.6695 (mtt90) REVERT: D 278 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7950 (p-90) REVERT: D 398 GLU cc_start: 0.8773 (tp30) cc_final: 0.8157 (tt0) REVERT: D 542 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: D 585 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5806 (p-80) REVERT: A 107 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7987 (ptmt) REVERT: A 187 LYS cc_start: 0.8300 (mtpt) cc_final: 0.8064 (mtpt) REVERT: A 308 GLU cc_start: 0.6479 (pm20) cc_final: 0.5667 (pt0) REVERT: A 389 TYR cc_start: 0.8239 (t80) cc_final: 0.8003 (t80) REVERT: A 545 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8115 (tt) REVERT: A 605 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8026 (ptpt) REVERT: A 719 ARG cc_start: 0.8432 (mmt-90) cc_final: 0.8214 (mmt-90) REVERT: A 765 SER cc_start: 0.8438 (t) cc_final: 0.7873 (p) REVERT: A 877 LYS cc_start: 0.7051 (tptm) cc_final: 0.6561 (mtpp) REVERT: A 899 ILE cc_start: 0.6696 (tt) cc_final: 0.6479 (tt) REVERT: A 927 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7176 (tt) REVERT: A 972 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6569 (mm-30) REVERT: A 1463 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.6941 (ttp80) REVERT: A 1487 TRP cc_start: 0.8065 (p-90) cc_final: 0.7709 (p-90) outliers start: 79 outliers final: 40 residues processed: 213 average time/residue: 0.1115 time to fit residues: 35.3584 Evaluate side-chains 197 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 278 TRP 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 594 PHE 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 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 314 ASP 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 514 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 542 ASP 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 684 THR Chi-restraints excluded: chain A residue 700 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 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139316 restraints weight = 16881.331| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.00 r_work: 0.3450 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15718 Z= 0.143 Angle : 0.696 11.012 21527 Z= 0.317 Chirality : 0.060 0.557 2432 Planarity : 0.004 0.046 2558 Dihedral : 12.014 175.656 2594 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.21 % Allowed : 24.66 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1832 helix: 1.41 (0.20), residues: 667 sheet: -1.00 (0.34), residues: 219 loop : -1.17 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.013 0.001 PHE D 289 TRP 0.037 0.001 TRP A 330 HIS 0.006 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (15702) covalent geometry : angle 0.68939 / 0.32 (21506) hydrogen bonds : bond 0.03366 / 2.22 ( 606) hydrogen bonds : angle 4.32479 / 3.16 ( 1705) metal coordination : bond 0.00932 / 0.75 ( 16) metal coordination : angle 3.24710 / 2.34 ( 21) *********************** 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 235 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 0.411 Fit side-chains REVERT: D 260 ARG cc_start: 0.6942 (mtt90) cc_final: 0.6710 (mtt90) REVERT: D 278 TRP cc_start: 0.8203 (OUTLIER) cc_final: 0.7977 (p-90) REVERT: D 542 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: D 585 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5817 (p-80) REVERT: A 141 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7083 (mttp) REVERT: A 214 GLU cc_start: 0.7458 (pm20) cc_final: 0.7045 (mm-30) REVERT: A 308 GLU cc_start: 0.6398 (pm20) cc_final: 0.5625 (pt0) REVERT: A 389 TYR cc_start: 0.8290 (t80) cc_final: 0.8072 (t80) REVERT: A 545 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8163 (tt) REVERT: A 605 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8049 (ptpt) REVERT: A 719 ARG cc_start: 0.8427 (mmt-90) cc_final: 0.8117 (mmt-90) REVERT: A 765 SER cc_start: 0.8471 (t) cc_final: 0.7936 (p) REVERT: A 877 LYS cc_start: 0.7057 (tptm) cc_final: 0.6553 (mtpp) REVERT: A 899 ILE cc_start: 0.6544 (tt) cc_final: 0.6266 (tt) REVERT: A 972 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6573 (mm-30) REVERT: A 1487 TRP cc_start: 0.8105 (p-90) cc_final: 0.7771 (p-90) outliers start: 72 outliers final: 45 residues processed: 217 average time/residue: 0.1161 time to fit residues: 37.2911 Evaluate side-chains 202 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 278 TRP 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 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 279 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU 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 514 LEU Chi-restraints excluded: chain A residue 540 VAL 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 684 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER 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 1582 VAL Chi-restraints excluded: chain A residue 1601 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN A 179 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133187 restraints weight = 17071.586| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.04 r_work: 0.3352 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15718 Z= 0.243 Angle : 0.821 11.510 21527 Z= 0.371 Chirality : 0.068 0.706 2432 Planarity : 0.004 0.043 2558 Dihedral : 12.281 165.606 2594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.78 % Allowed : 24.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1832 helix: 1.12 (0.20), residues: 672 sheet: -1.37 (0.32), residues: 233 loop : -1.30 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1581 TYR 0.016 0.002 TYR D 607 PHE 0.019 0.002 PHE D 324 TRP 0.054 0.002 TRP A 330 HIS 0.005 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (15702) covalent geometry : angle 0.81140 / 0.37 (21506) hydrogen bonds : bond 0.03833 / 2.53 ( 606) hydrogen bonds : angle 4.64093 / 3.39 ( 1705) metal coordination : bond 0.00868 / 0.64 ( 16) metal coordination : angle 4.10871 / 3.15 ( 21) *********************** 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 233 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 0.553 Fit side-chains REVERT: D 174 CYS cc_start: 0.7885 (t) cc_final: 0.7354 (t) REVERT: D 260 ARG cc_start: 0.6827 (mtt90) cc_final: 0.6601 (mtt90) REVERT: D 398 GLU cc_start: 0.8824 (tp30) cc_final: 0.8288 (tt0) REVERT: D 542 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6437 (m-80) REVERT: D 585 HIS cc_start: 0.6478 (OUTLIER) cc_final: 0.6116 (p-80) REVERT: A 107 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8235 (ptmt) REVERT: A 141 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7806 (mttp) REVERT: A 214 GLU cc_start: 0.7509 (pm20) cc_final: 0.6948 (mm-30) REVERT: A 605 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7908 (ptpt) REVERT: A 765 SER cc_start: 0.8546 (t) cc_final: 0.7955 (p) REVERT: A 899 ILE cc_start: 0.6575 (tt) cc_final: 0.6297 (tt) REVERT: A 972 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6748 (mm-30) REVERT: A 1463 ARG cc_start: 0.8560 (ttm110) cc_final: 0.7217 (ttp-170) outliers start: 80 outliers final: 52 residues processed: 215 average time/residue: 0.1176 time to fit residues: 37.4551 Evaluate side-chains 205 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 GLU 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 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 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 150 ASP Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 279 VAL 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 540 VAL 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 750 CYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER 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 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1517 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 107 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 83 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN A 179 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.179589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138593 restraints weight = 16837.504| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.03 r_work: 0.3458 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15718 Z= 0.128 Angle : 0.692 12.260 21527 Z= 0.316 Chirality : 0.057 0.524 2432 Planarity : 0.004 0.044 2558 Dihedral : 12.249 175.914 2594 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.77 % Allowed : 25.38 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1832 helix: 1.39 (0.20), residues: 668 sheet: -1.27 (0.34), residues: 217 loop : -1.23 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.016 0.001 PHE D 491 TRP 0.041 0.002 TRP A 330 HIS 0.005 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15702) covalent geometry : angle 0.68527 / 0.32 (21506) hydrogen bonds : bond 0.03280 / 2.14 ( 606) hydrogen bonds : angle 4.31757 / 3.16 ( 1705) metal coordination : bond 0.01107 / 0.91 ( 16) metal coordination : angle 3.11335 / 2.21 ( 21) *********************** 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 222 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 0.559 Fit side-chains REVERT: D 260 ARG cc_start: 0.6832 (mtt90) cc_final: 0.6598 (mtt90) REVERT: D 278 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7970 (p-90) REVERT: D 490 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7049 (p0) REVERT: D 542 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: D 585 HIS cc_start: 0.6118 (OUTLIER) cc_final: 0.5771 (p-80) REVERT: A 141 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7954 (mmtm) REVERT: A 214 GLU cc_start: 0.7507 (pm20) cc_final: 0.6969 (mm-30) REVERT: A 389 TYR cc_start: 0.8291 (t80) cc_final: 0.8022 (t80) REVERT: A 545 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 605 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8150 (ptpt) REVERT: A 765 SER cc_start: 0.8383 (t) cc_final: 0.7892 (p) REVERT: A 877 LYS cc_start: 0.6982 (tptm) cc_final: 0.6483 (mtpp) REVERT: A 972 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6635 (mm-30) REVERT: A 1463 ARG cc_start: 0.8565 (ttm110) cc_final: 0.7108 (ttp-170) REVERT: A 1510 GLU cc_start: 0.7379 (pt0) cc_final: 0.7162 (pt0) outliers start: 66 outliers final: 41 residues processed: 206 average time/residue: 0.1295 time to fit residues: 39.8562 Evaluate side-chains 200 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 278 TRP 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 490 ASP 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 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 179 ASN Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 210 THR 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 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 514 LEU Chi-restraints excluded: chain A residue 540 VAL 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 684 THR 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 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 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL 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 153 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136162 restraints weight = 17101.902| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.06 r_work: 0.3415 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15718 Z= 0.160 Angle : 0.717 11.775 21527 Z= 0.327 Chirality : 0.060 0.544 2432 Planarity : 0.004 0.043 2558 Dihedral : 12.249 171.046 2594 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.56 % Allowed : 25.60 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1832 helix: 1.31 (0.20), residues: 674 sheet: -1.33 (0.32), residues: 237 loop : -1.23 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.014 0.001 PHE D 491 TRP 0.034 0.002 TRP A1530 HIS 0.009 0.001 HIS A1484 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (15702) covalent geometry : angle 0.70997 / 0.33 (21506) hydrogen bonds : bond 0.03284 / 2.16 ( 606) hydrogen bonds : angle 4.34129 / 3.18 ( 1705) metal coordination : bond 0.00857 / 0.68 ( 16) metal coordination : angle 3.30146 / 2.45 ( 21) *********************** 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 218 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 0.555 Fit side-chains REVERT: D 260 ARG cc_start: 0.6822 (mtt90) cc_final: 0.6576 (mtt90) REVERT: D 398 GLU cc_start: 0.8753 (tp30) cc_final: 0.8201 (tt0) REVERT: D 542 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: D 585 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.5732 (p-80) REVERT: D 630 ASP cc_start: 0.7830 (p0) cc_final: 0.7404 (p0) REVERT: A 107 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8178 (ptmt) REVERT: A 141 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7138 (mttm) REVERT: A 214 GLU cc_start: 0.7453 (pm20) cc_final: 0.6929 (mm-30) REVERT: A 389 TYR cc_start: 0.8290 (t80) cc_final: 0.8043 (t80) REVERT: A 545 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 605 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8142 (ptpt) REVERT: A 765 SER cc_start: 0.8507 (t) cc_final: 0.7949 (p) REVERT: A 877 LYS cc_start: 0.7106 (tptm) cc_final: 0.6564 (mtpp) REVERT: A 972 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6610 (mm-30) REVERT: A 1463 ARG cc_start: 0.8618 (ttm110) cc_final: 0.7153 (ttp-170) outliers start: 63 outliers final: 48 residues processed: 204 average time/residue: 0.1316 time to fit residues: 39.3501 Evaluate side-chains 204 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 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 107 LYS 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 279 VAL Chi-restraints excluded: chain A residue 310 VAL 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 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 540 VAL 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 684 THR Chi-restraints excluded: chain A residue 700 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 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 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 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 97 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 154 optimal weight: 0.0270 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.180269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139437 restraints weight = 16738.025| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.06 r_work: 0.3466 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15718 Z= 0.127 Angle : 0.681 12.622 21527 Z= 0.312 Chirality : 0.057 0.501 2432 Planarity : 0.004 0.044 2558 Dihedral : 12.231 176.753 2594 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.41 % Allowed : 25.74 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1832 helix: 1.47 (0.20), residues: 667 sheet: -1.21 (0.33), residues: 228 loop : -1.23 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.014 0.001 TYR D 607 PHE 0.017 0.001 PHE D 289 TRP 0.026 0.001 TRP A1530 HIS 0.005 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15702) covalent geometry : angle 0.67537 / 0.31 (21506) hydrogen bonds : bond 0.03104 / 2.02 ( 606) hydrogen bonds : angle 4.28408 / 3.17 ( 1705) metal coordination : bond 0.00949 / 0.78 ( 16) metal coordination : angle 2.98177 / 2.14 ( 21) *********************** 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 214 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 153 time to evaluate : 0.571 Fit side-chains REVERT: D 260 ARG cc_start: 0.6846 (mtt90) cc_final: 0.6603 (mtt90) REVERT: D 278 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.7957 (p-90) REVERT: D 542 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: D 585 HIS cc_start: 0.6073 (OUTLIER) cc_final: 0.5689 (p-80) REVERT: D 630 ASP cc_start: 0.7825 (p0) cc_final: 0.7349 (p0) REVERT: A 141 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.6993 (mttm) REVERT: A 214 GLU cc_start: 0.7413 (pm20) cc_final: 0.6937 (mm-30) REVERT: A 389 TYR cc_start: 0.8270 (t80) cc_final: 0.8032 (t80) REVERT: A 545 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 696 ASN cc_start: 0.8254 (t0) cc_final: 0.8053 (t0) REVERT: A 765 SER cc_start: 0.8425 (t) cc_final: 0.7910 (p) REVERT: A 877 LYS cc_start: 0.7092 (tptm) cc_final: 0.6517 (mtpp) REVERT: A 1463 ARG cc_start: 0.8608 (ttm110) cc_final: 0.7141 (ttp80) outliers start: 61 outliers final: 46 residues processed: 198 average time/residue: 0.1418 time to fit residues: 41.2455 Evaluate side-chains 200 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 278 TRP Chi-restraints excluded: chain D residue 328 LEU 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 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 210 THR Chi-restraints excluded: chain A residue 310 VAL 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 513 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 684 THR 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 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 1468 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1507 VAL 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 79 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 181 optimal weight: 0.0870 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139646 restraints weight = 16850.334| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.06 r_work: 0.3461 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15718 Z= 0.128 Angle : 0.684 13.139 21527 Z= 0.313 Chirality : 0.057 0.489 2432 Planarity : 0.004 0.044 2558 Dihedral : 12.204 175.827 2594 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.05 % Allowed : 26.32 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1832 helix: 1.49 (0.20), residues: 668 sheet: -1.18 (0.33), residues: 228 loop : -1.20 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1581 TYR 0.015 0.001 TYR A 702 PHE 0.017 0.001 PHE D 289 TRP 0.024 0.001 TRP A1530 HIS 0.005 0.001 HIS A1484 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15702) covalent geometry : angle 0.67652 / 0.31 (21506) hydrogen bonds : bond 0.03049 / 2.00 ( 606) hydrogen bonds : angle 4.27348 / 3.16 ( 1705) metal coordination : bond 0.01183 / 0.98 ( 16) metal coordination : angle 3.28290 / 2.34 ( 21) ********************** 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 206 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.569 Fit side-chains REVERT: D 260 ARG cc_start: 0.6796 (mtt90) cc_final: 0.6556 (mtt90) REVERT: D 278 TRP cc_start: 0.8125 (OUTLIER) cc_final: 0.7911 (p-90) REVERT: D 398 GLU cc_start: 0.8713 (tp30) cc_final: 0.8120 (tt0) REVERT: D 542 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6343 (m-80) REVERT: D 585 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.5708 (p-80) REVERT: A 141 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7051 (mttp) REVERT: A 214 GLU cc_start: 0.7385 (pm20) cc_final: 0.6939 (mm-30) REVERT: A 389 TYR cc_start: 0.8292 (t80) cc_final: 0.8061 (t80) REVERT: A 545 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 765 SER cc_start: 0.8461 (t) cc_final: 0.7964 (p) REVERT: A 877 LYS cc_start: 0.7017 (tptm) cc_final: 0.6461 (mtpp) REVERT: A 1441 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6406 (mm-30) REVERT: A 1463 ARG cc_start: 0.8590 (ttm110) cc_final: 0.7097 (ttp80) outliers start: 56 outliers final: 48 residues processed: 195 average time/residue: 0.1381 time to fit residues: 39.7726 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 : 0.505 ------------------------------------------------------------------------------- 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 278 TRP Chi-restraints excluded: chain D residue 328 LEU 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 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 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 310 VAL 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 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 684 THR 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 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 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 8 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.177733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137076 restraints weight = 16806.233| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.15 r_work: 0.3417 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15718 Z= 0.164 Angle : 0.720 12.576 21527 Z= 0.329 Chirality : 0.060 0.509 2432 Planarity : 0.004 0.043 2558 Dihedral : 12.264 173.022 2594 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.56 % Allowed : 25.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1832 helix: 1.37 (0.20), residues: 673 sheet: -1.25 (0.32), residues: 236 loop : -1.27 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1581 TYR 0.015 0.001 TYR D 607 PHE 0.018 0.001 PHE D 289 TRP 0.038 0.002 TRP A1530 HIS 0.005 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (15702) covalent geometry : angle 0.71289 / 0.33 (21506) hydrogen bonds : bond 0.03201 / 2.11 ( 606) hydrogen bonds : angle 4.37591 / 3.22 ( 1705) metal coordination : bond 0.00822 / 0.65 ( 16) metal coordination : angle 3.37058 / 2.48 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3728.80 seconds wall clock time: 64 minutes 37.94 seconds (3877.94 seconds total)